From 361a72b833c221dd2c48571154d6dbc90bbb6459 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 12:57:35 +0000 Subject: [PATCH 01/20] Adding NF-TEST files --- assets/schema_input.json | 3 +++ assets/test.yaml | 4 ++-- conf/base.config | 6 ++--- conf/test.config | 25 ++++++++++++++------ nf-test.config | 16 +++++++++++++ tests/main.nf.test | 49 ++++++++++++++++++++++++++++++++++++++++ tests/main.nf.test.snap | 33 +++++++++++++++++++++++++++ workflows/ear.nf | 48 ++++++++++++++++++++------------------- 8 files changed, 149 insertions(+), 35 deletions(-) create mode 100644 nf-test.config create mode 100644 tests/main.nf.test create mode 100644 tests/main.nf.test.snap diff --git a/assets/schema_input.json b/assets/schema_input.json index 61d2b74..2b6741b 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -53,6 +53,9 @@ }, "fastk_ktab": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.ktab$", "errorMessage": "Directory containing ktab files" } } diff --git a/assets/test.yaml b/assets/test.yaml index 0f5f6ed..14b0b50 100755 --- a/assets/test.yaml +++ b/assets/test.yaml @@ -8,8 +8,8 @@ reference_haplotigs: /home/runner/work/ear/ear/TreeValTinyData/assembly/draft/gr mapped_bam: [] merquryfk: - fastk_hist: "./" - fastk_ktab: "./" + fastk_hist: "./EMPTY.hist" + fastk_ktab: "./EMPTY.ktab" # Used by both subpipelines longread: diff --git a/conf/base.config b/conf/base.config index 4b330f4..8d7339e 100644 --- a/conf/base.config +++ b/conf/base.config @@ -20,13 +20,13 @@ process { maxErrors = '-1' withName: "SANGER_TOL_CPRETEXT|SANGER_TOL_BTK" { - time = { check_max( 70.h * task.attempt, 'time' ) } + time = { check_max( 8.d * task.attempt, 'time' ) } } withName: "MINIMAP2_ALIGN_SE" { cpus = { check_max( 16 , 'cpus' ) } - memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 60 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * task.attempt ) , 'memory') } - time = { check_max( 1.h * ( reference.size() < 1e9 ? 15 : reference.size() < 10e9 ? 30 : 48), 'time' ) } + memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 50 : Math.ceil( ( reference.size() / 1e+9 ) * 25 ) * task.attempt ) , 'memory') } + time = { check_max( 1.h * ( reference.size() < 1e9 ? 20 : reference.size() < 10e9 ? 35 : 48), 'time' ) } } // Process-specific resource requirements diff --git a/conf/test.config b/conf/test.config index 06d069f..2fc0011 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,26 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + +process { + resourceLimits = [ + cpus: 4, + memory: '10.GB', + time: '1.h' + ] +} + params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' + config_profile_name = 'Full test profile' + config_profile_description = 'Full test dataset to check pipeline function' + // Input data for full size test // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - input = "${projectDir}/assets/test.yaml" - outdir = "results" + max_cpus = 4 + max_memory = '10.GB' + max_time = '1.h' + input = "${baseDir}/assets/test.yaml" + steps = "btk,cpretext,merquryfk" } diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 0000000..cc4372f --- /dev/null +++ b/nf-test.config @@ -0,0 +1,16 @@ +config { + testsDir "tests" + workDir ".nf-test" + libDir "tests/lib" + withTrace true + autoSort false + + options "-dump-channels" + + plugins { + load "nft-utils@0.0.3" + } + + configFile "conf/test.config" + profile "test" +} diff --git a/tests/main.nf.test b/tests/main.nf.test new file mode 100644 index 0000000..556f956 --- /dev/null +++ b/tests/main.nf.test @@ -0,0 +1,49 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "pipeline" + tag "pipeline_sanger_tol" + tag "full" + + test("Minimal run | No SANGER-TOL-* nested pipelines") { + + when { + params { + outdir = "${outputDir}" + } + } + + then { + + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ["pipeline_info/*.{html,json,txt}"]) + + def gfastats = getAllFilesFromDir(params.outdir, include: ['gfastats/_summary']) + + //def merquryfk = getAllFilesFromDir(params.outdir, include: ['merquryfk/*']) + + assertAll ( + {assert workflow.success}, + {assert snapshot( + // Test for number of successful processes - should be 29 for a full run + workflow.trace.succeeded().size(), + + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + + stable_name, + // GFASTATS should be a stable file as it is measuring metrics of the files + // so nothing special needs to be done + + gfastats.size(), + gfastats, + + // MERQURY_FK is running statistics on the input files + // input files are also split between the two main input haps + // need to actually test merqury first + //merquryfk, + + ).match()}, + ) + } + } +} diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap new file mode 100644 index 0000000..7329d59 --- /dev/null +++ b/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Minimal run | No SANGER-TOL-* nested pipelines": { + "content": [ + 2, + { + "CAT_CAT": { + "pigz": "2.3.4" + }, + "GFASTATS": { + "gfastats": "1.3.6" + }, + "Workflow": { + "sanger-tol/ear": "v0.6.2" + } + }, + [ + "gfastats", + "gfastats/grTriPseu1.assembly_summary", + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml" + ], + 0, + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2025-02-07T12:39:47.429262" + } +} \ No newline at end of file diff --git a/workflows/ear.nf b/workflows/ear.nf index a37966c..fb9154e 100644 --- a/workflows/ear.nf +++ b/workflows/ear.nf @@ -50,7 +50,7 @@ workflow EAR { // // MODULE: YAML_INPUT - // - YAML_INPUT SHOULD BE REWORKED TO BE SMARTER + // TODO: REPLACE WITH -params-input // YAML_INPUT(ch_input) @@ -120,7 +120,6 @@ workflow EAR { // LOGIC: STEP TO STOP MERQURY_FK RUNNING IF SPECIFIED BY USER // if (!exclude_steps.contains('merquryfk')) { - // // MODULE: MERQURYFK PLOTS OF GENOME // @@ -132,32 +131,32 @@ workflow EAR { ch_versions = ch_versions.mix( MERQURYFK_MERQURYFK.out.versions ) } - // - // LOGIC: IF A MAPPED BAM FILE EXISTS AND THE FLAG `mapped` IS TRUE - // SKIP THE MAPPING SUBWORKFLOW - // - if (!params.mapped) { - // - // SUBWORKFLOW: MAIN_MAPPING CONTAINS ALL THE MAPPING LOGIC - // This allows us to more esily bypass the mapping if we already have a sorted and mapped bam - // - MAIN_MAPPING ( - YAML_INPUT.out.sample_id, - YAML_INPUT.out.longread_type, - YAML_INPUT.out.reference_hap1, - YAML_INPUT.out.pacbio_tuple, - ) - ch_versions = ch_versions.mix( MAIN_MAPPING.out.versions ) - ch_mapped_bam = MAIN_MAPPING.out.mapped_bam - } else { - ch_mapped_bam = YAML_INPUT.out.mapped_bam - } - // // LOGIC: STEP TO STOP BTK RUNNING IF SPECIFIED BY USER // if (!exclude_steps.contains('btk')) { + // + // LOGIC: IF A MAPPED BAM FILE EXISTS AND THE FLAG `mapped` IS TRUE + // SKIP THE MAPPING SUBWORKFLOW + // + if (!params.mapped) { + // + // SUBWORKFLOW: MAIN_MAPPING CONTAINS ALL THE MAPPING LOGIC + // This allows us to more esily bypass the mapping if we already have a sorted and mapped bam + // + MAIN_MAPPING ( + YAML_INPUT.out.sample_id, + YAML_INPUT.out.longread_type, + YAML_INPUT.out.reference_hap1, + YAML_INPUT.out.pacbio_tuple, + ) + ch_versions = ch_versions.mix( MAIN_MAPPING.out.versions ) + ch_mapped_bam = MAIN_MAPPING.out.mapped_bam + } else { + ch_mapped_bam = YAML_INPUT.out.mapped_bam + } + // // MODULE: GENERATE_SAMPLESHEET creates a csv for the blobtoolkit pipeline @@ -187,6 +186,7 @@ workflow EAR { ch_versions = ch_versions.mix(SANGER_TOL_BTK.out.versions) } + // // LOGIC: STEP TO STOP CURATION_PRETEXT RUNNING IF SPECIFIED BY USER // @@ -207,6 +207,7 @@ workflow EAR { ch_versions = ch_versions.mix( SANGER_TOL_CPRETEXT.out.versions ) } + // // Collate and save software versions // @@ -218,6 +219,7 @@ workflow EAR { newLine: true ).set { ch_collated_versions } + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) From 476152038668af2332301977134a59292126b68b Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 13:01:04 +0000 Subject: [PATCH 02/20] Updating CICD --- .github/workflows/ci.yml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a21e2f4..0304912 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,10 +45,13 @@ jobs: cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-hap.fa cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa - - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix - # Skip BTK and CPRETEXT as they are already tested on their repos. + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + + # Test the component + - name: Run nf-test run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --steps btk,cpretext,merquryfk + nf-test test \ + --profile="docker" \ + --debug \ + --verbose From 9d01433220bd90ec4b7024f3ce3152771bb39718 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 13:03:02 +0000 Subject: [PATCH 03/20] Reduce limit of 8.d to 2.d --- conf/base.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 8d7339e..865625d 100644 --- a/conf/base.config +++ b/conf/base.config @@ -20,7 +20,7 @@ process { maxErrors = '-1' withName: "SANGER_TOL_CPRETEXT|SANGER_TOL_BTK" { - time = { check_max( 8.d * task.attempt, 'time' ) } + time = { check_max( 2.d * task.attempt, 'time' ) } } withName: "MINIMAP2_ALIGN_SE" { From c5e7ea4fa0fecd3478081023c488f7bb50c5e775 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 13:35:03 +0000 Subject: [PATCH 04/20] updates --- .github/workflows/branch.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index e3f6dae..7ac1e04 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -3,7 +3,7 @@ name: nf-core branch protection # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: [main] jobs: test: From 8edc609bc16a46fd3f4c9ff1254e8124f5cecf12 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 14:24:15 +0000 Subject: [PATCH 05/20] Update to template --- conf/test.config | 4 --- .../local/utils_nfcore_ear_pipeline/main.nf | 36 +++++++++---------- 2 files changed, 16 insertions(+), 24 deletions(-) diff --git a/conf/test.config b/conf/test.config index 2fc0011..db0d1a3 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,10 +26,6 @@ params { // Input data for full size test // Limit resources so that this can run on GitHub Actions - max_cpus = 4 - max_memory = '10.GB' - max_time = '1.h' - input = "${baseDir}/assets/test.yaml" steps = "btk,cpretext,merquryfk" } diff --git a/subworkflows/local/utils_nfcore_ear_pipeline/main.nf b/subworkflows/local/utils_nfcore_ear_pipeline/main.nf index 3bef592..9fd6da0 100644 --- a/subworkflows/local/utils_nfcore_ear_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_ear_pipeline/main.nf @@ -76,28 +76,24 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - Channel - .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { - validateInputSamplesheet(it) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } + + // Channel + // .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + // .map { + // meta, file + // } + // .groupTuple() + // .map { samplesheet -> + // validateInputSamplesheet(samplesheet) + // } + // .map { + // meta, fastqs -> + // return [ meta, fastqs.flatten() ] + // } + // .set { ch_samplesheet } emit: - samplesheet = ch_samplesheet + samplesheet = params.input versions = ch_versions } From 86ccafcb75b8dc81a86b49b83cb8c70646f4b151 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 14:29:31 +0000 Subject: [PATCH 06/20] Update --- assets/test-local.yaml | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 assets/test-local.yaml diff --git a/assets/test-local.yaml b/assets/test-local.yaml new file mode 100755 index 0000000..c5e9ab5 --- /dev/null +++ b/assets/test-local.yaml @@ -0,0 +1,33 @@ +# General Vales for all subpiplines and modules +assembly_id: grTriPseu1 +reference_hap1: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1.fa +reference_hap2: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-hap.fa +reference_haplotigs: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa + +# If a mapped bam already exists use the below + --mapped TRUE on the nextflow command else ignore. +mapped_bam: [] + +merquryfk: + fastk_hist: "./EMPTY.hist" + fastk_ktab: "./EMPTY.ktab" + +# Used by both subpipelines +longread: + type: hifi + dir: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/genomic_data/pacbio/ + +curationpretext: + aligner: minimap2 + telomere_motif: TTAGGG + hic_dir: /home/runner/work/ear/ear/TreeValTinyData/genomic_data/hic-arima/ +btk: + taxid: 352914 + gca_accession: GCA_0001 + lineages: "fungi_odb10" + nt_database: /home/runner/work/ascc/ascc/NT_database/ + nt_database_prefix: 18S_fungal_sequences + diamond_uniprot_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd + diamond_nr_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd + ncbi_taxonomy_path: /home/runner/work/ascc/ascc/ncbi_taxdump/ + ncbi_rankedlineage_path: /home/runner/work/ascc/ascc/ncbi_taxdump/rankedlineage.dmp + config: /home/runner/work/ear/ear/conf/sanger-tol-btk.config From e8ca48757b413130050acc685cf165cf83253377 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 14:42:27 +0000 Subject: [PATCH 07/20] Template update for nf-core/tools version 3.2.0 --- .editorconfig | 4 + .github/CONTRIBUTING.md | 24 +- .github/ISSUE_TEMPLATE/bug_report.yml | 32 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/branch.yml | 18 +- .github/workflows/ci.yml | 61 ++- .github/workflows/download_pipeline.yml | 92 +++-- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting.yml | 33 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 75 ---- .../workflows/template_version_comment.yml | 46 +++ .gitignore | 1 + .gitpod.yml | 14 +- .nf-core.yml | 28 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + .vscode/settings.json | 3 + CHANGELOG.md | 2 +- CITATIONS.md | 4 +- LICENSE | 2 +- README.md | 14 +- assets/multiqc_config.yml | 2 +- assets/schema_input.json | 2 +- conf/base.config | 36 +- conf/test.config | 15 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 10 - docs/usage.md | 47 +-- main.nf | 8 - modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 25 +- modules/nf-core/fastqc/meta.yml | 58 +-- modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- modules/nf-core/fastqc/tests/tags.yml | 2 - modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 16 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 24 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 151 ++++--- nextflow_schema.json | 81 +--- ro-crate-metadata.json | 295 ++++++++++++++ .../local/utils_nfcore_ear_pipeline/main.nf | 68 ++-- .../nf-core/utils_nextflow_pipeline/main.nf | 72 ++-- .../tests/main.workflow.nf.test | 10 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 367 ++++++++--------- .../tests/main.function.nf.test | 46 +-- .../tests/main.function.nf.test.snap | 30 -- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ---------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/ear.nf | 21 +- 65 files changed, 1821 insertions(+), 1257 deletions(-) delete mode 100644 .github/workflows/release-announcements.yml create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 .vscode/settings.json delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png delete mode 100644 modules/nf-core/fastqc/tests/tags.yml create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 ro-crate-metadata.json create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 72dda28..6d9b74c 100644 --- a/.editorconfig +++ b/.editorconfig @@ -31,3 +31,7 @@ indent_size = unset # ignore python and markdown [*.{py,md}] indent_style = unset + +# ignore ro-crate metadata files +[**/ro-crate-metadata.json] +insert_final_newline = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a199499..ba3fc31 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,4 +1,4 @@ -# sanger-tol/ear: Contributing Guidelines +# `sanger-tol/ear`: Contributing Guidelines Hi there! Many thanks for taking an interest in improving sanger-tol/ear. @@ -16,7 +16,7 @@ If you'd like to write some code for sanger-tol/ear, the standard workflow is as 1. Check that there isn't already an issue about your idea in the [sanger-tol/ear issues](https://github.com/sanger-tol/ear/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [sanger-tol/ear repository](https://github.com/sanger-tol/ear) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -37,7 +37,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -52,23 +52,23 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/master`. +- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. - Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. +- Open a pull-request from `patch` to `main`/`master` with the changes. ## Pipeline contribution conventions -To make the sanger-tol/ear code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. +To make the `sanger-tol/ear` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. ### Adding a new step If you wish to contribute a new step, please use the following coding standards: -1. Define the corresponding input channel into your new process from the expected previous process channel +1. Define the corresponding input channel into your new process from the expected previous process channel. 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -77,13 +77,13 @@ If you wish to contribute a new step, please use the following coding standards: ### Default values -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. +Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. @@ -96,7 +96,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index b6d8a80..19e671a 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,46 +9,34 @@ body: description: A clear and concise description of what the bug is. validations: required: true + - type: textarea id: command_used attributes: label: Command used and terminal output - description: Steps to reproduce the behaviour. Please paste the command you used - to launch the pipeline and the output from your terminal. + description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. render: console - placeholder: "$ nextflow run ... - + placeholder: | + $ nextflow run ... Some output where something broke - " - type: textarea id: files attributes: label: Relevant files - description: "Please drag and drop the relevant files here. Create a `.zip` archive - if the extension is not allowed. - - Your verbose log file `.nextflow.log` is often useful _(this is a hidden file - in the directory where you launched the pipeline)_ as well as custom Nextflow - configuration files. + description: | + Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. + Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. - " - type: textarea id: system attributes: label: System information - description: "* Nextflow version _(eg. 23.04.0)_ - + description: | + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ - * Executor _(eg. slurm, local, awsbatch)_ - - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, - or Apptainer)_ - + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of sanger-tol/ear _(eg. 1.1, 1.5, 1.8.2)_ - - " diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index e73beeb..b8bb012 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/e - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sanger-tol/ear/tree/master/.github/CONTRIBUTING.md) -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index e3f6dae..824fcf2 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,15 +1,17 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to `main`/`master` branch on the repository +# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: + - main + - master jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'sanger-tol/ear' run: | @@ -22,7 +24,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +34,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch. + The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e2003fe..39f710e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,9 +7,12 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -17,30 +20,68 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/ear') }}" runs-on: ubuntu-latest strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda + + - name: Set up Conda + if: matrix.profile == 'conda' + run: | + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d64..ab06316 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,14 +1,14 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main/master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -17,17 +17,34 @@ on: - edited - synchronize branches: + - main - master pull_request_target: branches: + - main - master env: NXF_ANSI_LOG: false jobs: + configure: + runs-on: ubuntu-latest + outputs: + REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} + REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} + REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} + steps: + - name: Get the repository name and current branch + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + download: runs-on: ubuntu-latest + needs: configure steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -35,52 +52,83 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | python -m pip install --upgrade pip pip install git+https://github.com/nf-core/tools.git@dev - - name: Get the repository name and current branch set as environment variable + - name: Make a cache directory for the container images run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + mkdir -p ./singularity_container_images - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" + + - name: Compare container image counts + run: | + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index cec728b..a717e0d 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe8..dbd52d5 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -31,27 +31,42 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} @@ -59,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23..95b6b6a 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml deleted file mode 100644 index 03ecfcf..0000000 --- a/.github/workflows/release-announcements.yml +++ /dev/null @@ -1,75 +0,0 @@ -name: release-announcements -# Automatic release toot and tweet anouncements -on: - release: - types: [published] - workflow_dispatch: - -jobs: - toot: - runs-on: ubuntu-latest - steps: - - name: get topics and convert to hashtags - id: get_topics - run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT - - - uses: rzr/fediverse-action@master - with: - access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} - host: "mstdn.science" # custom host if not "mastodon.social" (default) - # GitHub event payload - # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release - message: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - - ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics - - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - - bsky-post: - runs-on: ubuntu-latest - steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 - with: - post: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - env: - BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} - BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} - # diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 0000000..537529b --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,46 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + contains(env.OUTPUT, 'nf-core') + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitignore b/.gitignore index 5124c9a..a42ce01 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/.gitpod.yml b/.gitpod.yml index 105a182..83599f6 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,7 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: - extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - charliermarsh.ruff # Code linter Ruff + extensions: + - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index 9a35f55..011899a 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -4,24 +4,46 @@ lint: - assets/nf-core-ear_logo_light.png - docs/images/nf-core-ear_logo_light.png - docs/images/nf-core-ear_logo_dark.png + - lib/nfcore_external_java_deps.jar + - lib/NfcoreSchema.groovy + - lib/NfcoreTemplate.groovy + - lib/Utils.groovy + - lib/WorkflowMain.groovy - .github/ISSUE_TEMPLATE/config.yml - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml - conf/igenomes.config files_unchanged: + - LICENSE - CODE_OF_CONDUCT.md - assets/nf-core-ear_logo_light.png - docs/images/nf-core-ear_logo_light.png - docs/images/nf-core-ear_logo_dark.png - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - assets/email_template.html multiqc_config: - report_comment nextflow_config: - manifest.name - manifest.homePage -nf_core_version: 2.14.1 + - params.show_hidden_params + - params.schema_ignore_params + - params.validationSchemaIgnoreParams +nf_core_version: 3.2.0 repository_type: pipeline template: - prefix: sanger-tol - skip: + author: DLBPointon + description: ERGA Assembly Report pipeline + force: false + is_nfcore: false + name: ear + org: sanger-tol + outdir: . + skip_features: - igenomes + version: 0.6.2 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1d..1dec865 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.1.2" hooks: - id: editorconfig-checker alias: ec diff --git a/.prettierignore b/.prettierignore index 437d763..edd29f0 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,3 +10,4 @@ testing/ testing* *.pyc bin/ +ro-crate-metadata.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..a33b527 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "markdown.styles": ["public/vscode_markdown.css"] +} diff --git a/CHANGELOG.md b/CHANGELOG.md index c3d90bc..75b5c25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## v0.6.2 - [date] Initial release of sanger-tol/ear, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index c0cf948..fa12079 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/LICENSE b/LICENSE index 967fdcd..1c153cb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) DLBPointon +Copyright (c) The sanger-tol/ear team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 506512d..9c6fb8e 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,10 @@ +# sanger-tol/ear + [![GitHub Actions CI Status](https://github.com/sanger-tol/ear/actions/workflows/ci.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/sanger-tol/ear/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -20,10 +22,7 @@ - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage @@ -58,8 +57,7 @@ nextflow run sanger-tol/ear \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). ## Credits @@ -82,7 +80,7 @@ If you would like to contribute to this pipeline, please see the [contributing g An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. -This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE). +This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE). > **The nf-core framework for community-curated bioinformatics pipelines.** > diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 085a4c2..e777952 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the sanger-tol/ear + This report has been generated by the sanger-tol/ear analysis pipeline. report_section_order: "sanger-tol-ear-methods-description": diff --git a/assets/schema_input.json b/assets/schema_input.json index 8012bf6..a45c691 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/sanger-tol/ear/master/assets/schema_input.json", "title": "sanger-tol/ear pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index 4136c84..a7c30b8 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,46 +11,46 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/test.config b/conf/test.config index 024498b..5fe36a1 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,19 +10,20 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - } diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index 335ec21..d23efae 100644 --- a/docs/output.md +++ b/docs/output.md @@ -29,16 +29,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index 42521d3..28800df 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -55,7 +55,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run sanger-tol/ear --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run sanger-tol/ear --input ./samplesheet.csv --outdir ./results -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -73,9 +73,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -83,12 +82,11 @@ The above pipeline run specified with a params file in yaml format: nextflow run sanger-tol/ear -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' -genome: 'GRCh37' <...> ``` @@ -104,23 +102,21 @@ nextflow pull sanger-tol/ear ### Reproducibility -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the [sanger-tol/ear releases page](https://github.com/sanger-tol/ear/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -128,16 +124,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -173,13 +168,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. @@ -197,14 +192,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index 96a8a81..74b8b6e 100644 --- a/main.nf +++ b/main.nf @@ -7,8 +7,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -18,7 +16,6 @@ nextflow.enable.dsl = 2 include { EAR } from './workflows/ear' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_ear_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_ear_pipeline' - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -41,10 +38,8 @@ workflow SANGERTOL_EAR { EAR ( samplesheet ) - emit: multiqc_report = EAR.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -55,13 +50,11 @@ workflow SANGERTOL_EAR { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, @@ -75,7 +68,6 @@ workflow { SANGERTOL_EAR ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index 99a74d8..36cd906 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38..691d4c7 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c8..033f415 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -1,5 +1,5 @@ process FASTQC { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" @@ -19,27 +19,30 @@ process FASTQC { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of old name and new name pairs to use for renaming in the bash while loop def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do + printf "%s %s\\n" ${rename_to} | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done fastqc \\ - $args \\ - --threads $task.cpus \\ - --memory $fastqc_memory \\ - $renamed_files + ${args} \\ + --threads ${task.cpus} \\ + --memory ${fastqc_memory} \\ + ${renamed_files} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e..2b2e62b 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -11,40 +11,50 @@ tools: FastQC gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other overrepresented sequences. homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4..e9d79a0 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c31..d5db309 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294..0000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb6..a27122c 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.27 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352..58d9313 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : + 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -44,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc3..b16c187 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242..33316a7 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd80..7b7c132 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2025-01-27T09:29:57.631982377" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2025-01-27T09:30:34.743726958" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2025-01-27T09:30:21.44383553" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 0000000..c537a6a --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index fc630a6..c8c7556 100644 --- a/nextflow.config +++ b/nextflow.config @@ -29,48 +29,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - - // Config options + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load sanger-tol/ear custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/ear.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/ear profiles: ${params.custom_config_base}/pipeline/ear.config") -} profiles { debug { dumpHashes = true @@ -85,7 +63,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -169,23 +147,35 @@ profiles { executor.name = 'local' executor.cpus = 4 executor.memory = 8.GB + process { + resourceLimits = [ + memory: 8.GB, + cpus : 4, + time : 1.h + ] + } } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" + +// Load sanger-tol/ear custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/ear.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' + -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. @@ -198,73 +188,74 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'sanger-tol/ear' - author = """DLBPointon""" + author = """DLBPointon""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead + contributors = [ + // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 + [ + name: 'DLBPointon', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + ] homePage = 'https://github.com/sanger-tol/ear' description = """ERGA Assembly Report pipeline""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '1.0dev' + defaultBranch = 'master' + nextflowVersion = '!>=24.04.2' + version = '0.6.2' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +validation { + defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs + help { + enabled = true + command = "nextflow run sanger-tol/ear -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index b0fd6d6..dd89230 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/sanger-tol/ear/master/nextflow_schema.json", "title": "sanger-tol/ear pipeline parameters", "description": "ERGA Assembly Report pipeline", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -91,41 +91,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -133,12 +98,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -214,49 +173,31 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", "hidden": true + }, + "trace_report_suffix": { + "type": "string", + "fa_icon": "far calendar", + "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", + "hidden": true } } } }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 0000000..a0d7f0b --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,295 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "GithubService": "https://w3id.org/ro/terms/test#GithubService", + "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", + "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", + "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", + "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", + "TestService": "https://w3id.org/ro/terms/test#TestService", + "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", + "TravisService": "https://w3id.org/ro/terms/test#TravisService", + "definition": "https://w3id.org/ro/terms/test#definition", + "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", + "instance": "https://w3id.org/ro/terms/test#instance", + "resource": "https://w3id.org/ro/terms/test#resource", + "runsOn": "https://w3id.org/ro/terms/test#runsOn" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "Stable", + "datePublished": "2025-02-07T14:42:23+00:00", + "description": "# sanger-tol/ear\n\n[![GitHub Actions CI Status](https://github.com/sanger-tol/ear/actions/workflows/ci.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/sanger-tol/ear/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/sanger-tol/ear)\n\n## Introduction\n\n**sanger-tol/ear** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run sanger-tol/ear \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Credits\n\nsanger-tol/ear was originally written by DLBPointon.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/sanger-tol/ear", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "mentions": [ + { + "@id": "#4cecab1b-edaa-47aa-b478-9bde79e72d84" + } + ], + "name": "sanger-tol/ear" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], + "dateCreated": "", + "dateModified": "2025-02-07T14:42:23Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": [ + "nf-core", + "nextflow" + ], + "license": [ + "MIT" + ], + "name": [ + "sanger-tol/ear" + ], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": [ + "https://github.com/sanger-tol/ear", + "https://nf-co.re/sanger-tol/ear/0.6.2/" + ], + "version": [ + "0.6.2" + ] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=24.04.2" + }, + { + "@id": "#4cecab1b-edaa-47aa-b478-9bde79e72d84", + "@type": "TestSuite", + "instance": [ + { + "@id": "#77d32351-db55-4de1-831b-b0e5b99d6477" + } + ], + "mainEntity": { + "@id": "main.nf" + }, + "name": "Test suite for sanger-tol/ear" + }, + { + "@id": "#77d32351-db55-4de1-831b-b0e5b99d6477", + "@type": "TestInstance", + "name": "GitHub Actions workflow for testing sanger-tol/ear", + "resource": "repos/sanger-tol/ear/actions/workflows/ci.yml", + "runsOn": { + "@id": "https://w3id.org/ro/terms/test#GithubService" + }, + "url": "https://api.github.com" + }, + { + "@id": "https://w3id.org/ro/terms/test#GithubService", + "@type": "TestService", + "name": "Github Actions", + "url": { + "@id": "https://github.com" + } + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@type": "File", + "description": "The license - should be MIT" + }, + { + "@id": "CITATIONS.md", + "@type": "File", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + } + ] +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_ear_pipeline/main.nf b/subworkflows/local/utils_nfcore_ear_pipeline/main.nf index 3bef592..cf0f140 100644 --- a/subworkflows/local/utils_nfcore_ear_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_ear_pipeline/main.nf @@ -8,29 +8,25 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -54,16 +50,10 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) // @@ -76,8 +66,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -87,8 +78,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -102,9 +93,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -119,19 +110,26 @@ workflow PIPELINE_COMPLETION { multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def multiqc_reports = multiqc_report.toList() // // Completion email and summary // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_reports.getVal(), + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -143,9 +141,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -155,14 +153,13 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } return [ metas[0], fastqs ] } - // // Generate methods description for MultiQC // @@ -193,7 +190,7 @@ def toolBibliographyText() { } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = workflow.toMap() meta["manifest_map"] = workflow.manifest.toMap() @@ -204,8 +201,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -226,3 +225,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28..d6e593e 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,18 +2,13 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -76,13 +71,13 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,37 +85,42 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce..02dbf09 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926b..a09572e 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c3..bfd2587 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,17 +2,13 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -52,39 +45,22 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +78,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -113,8 +89,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -122,11 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { processVersionsFromYAML(it) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -134,61 +106,40 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -200,79 +151,76 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - return mqc_report } // @@ -281,26 +229,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -317,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -337,40 +294,45 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -378,15 +340,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") + } + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -395,21 +359,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -434,13 +407,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f..f117040 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232..02c6701 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 0000000..4994303 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 0000000..f7d9f02 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 0000000..8fb3016 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 0000000..0907ac5 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c..331e0d2 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b0..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cff..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/ear.nf b/workflows/ear.nf index 67d3ef6..ab97247 100644 --- a/workflows/ear.nf +++ b/workflows/ear.nf @@ -3,10 +3,9 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_ear_pipeline' @@ -21,12 +20,10 @@ workflow EAR { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // // MODULE: Run FastQC // @@ -42,11 +39,12 @@ workflow EAR { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'ear_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -62,15 +60,14 @@ workflow EAR { summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +80,14 @@ workflow EAR { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From a27fed3a6866c933e609c5b6df6bc67a711cf106 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 14:57:36 +0000 Subject: [PATCH 08/20] Template update to v3 --- .../local/utils_nfcore_ear_pipeline/main.nf | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/subworkflows/local/utils_nfcore_ear_pipeline/main.nf b/subworkflows/local/utils_nfcore_ear_pipeline/main.nf index cf0f140..8b66220 100644 --- a/subworkflows/local/utils_nfcore_ear_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_ear_pipeline/main.nf @@ -67,28 +67,28 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // - Channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { samplesheet -> - validateInputSamplesheet(samplesheet) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } + // Channel + // .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + // .map { + // meta, fastq_1, fastq_2 -> + // if (!fastq_2) { + // return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + // } else { + // return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + // } + // } + // .groupTuple() + // .map { samplesheet -> + // validateInputSamplesheet(samplesheet) + // } + // .map { + // meta, fastqs -> + // return [ meta, fastqs.flatten() ] + // } + // .set { ch_samplesheet } emit: - samplesheet = ch_samplesheet + samplesheet = params.input versions = ch_versions } From e88f971eced1331e7128da4e86bf6867eed5fcce Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 15:16:19 +0000 Subject: [PATCH 09/20] commenting out some of the template --- main.nf | 35 +++++++++++++++++------------------ 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/main.nf b/main.nf index cf41a92..641a381 100644 --- a/main.nf +++ b/main.nf @@ -53,33 +53,32 @@ workflow { // // SUBWORKFLOW: Run initialisation tasks // - PIPELINE_INITIALISATION ( - params.version, - params.validate_params, - params.monochrome_logs, - args, - params.outdir, - params.input - ) + // PIPELINE_INITIALISATION ( + // params.version, + // params.validate_params, + // params.monochrome_logs, + // args, + // params.outdir, + // params.input + // ) // // WORKFLOW: Run main workflow // SANGERTOL_EAR ( - PIPELINE_INITIALISATION.out.samplesheet + params.input ) // // SUBWORKFLOW: Run completion tasks // - PIPELINE_COMPLETION ( - params.email, - params.email_on_fail, - params.plaintext_email, - params.outdir, - params.monochrome_logs, - params.hook_url, - SANGERTOL_EAR.out.multiqc_report - ) + // PIPELINE_COMPLETION ( + // params.email, + // params.email_on_fail, + // params.plaintext_email, + // params.outdir, + // params.monochrome_logs, + // params.hook_url + // ) } From 966da01cb3381f8521d31d71c6d8903a48fe1335 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 16:49:40 +0000 Subject: [PATCH 10/20] Update snapshot --- conf/test.config | 2 +- tests/main.nf.test | 4 ++-- tests/main.nf.test.snap | 12 ++++++------ 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/conf/test.config b/conf/test.config index db0d1a3..b1b6eeb 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,6 +26,6 @@ params { // Input data for full size test // Limit resources so that this can run on GitHub Actions - input = "${baseDir}/assets/test.yaml" + input = "${baseDir}/assets/test-local.yaml" steps = "btk,cpretext,merquryfk" } diff --git a/tests/main.nf.test b/tests/main.nf.test index 556f956..f3002ca 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ["pipeline_info/*.{html,json,txt}"]) - def gfastats = getAllFilesFromDir(params.outdir, include: ['gfastats/_summary']) + def gfastats = getAllFilesFromDir(params.outdir, include: ['gfastats/*_summary']) //def merquryfk = getAllFilesFromDir(params.outdir, include: ['merquryfk/*']) @@ -28,7 +28,7 @@ nextflow_pipeline { // Test for number of successful processes - should be 29 for a full run workflow.trace.succeeded().size(), - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/ear_software_mqc_versions.yml"), stable_name, // GFASTATS should be a stable file as it is measuring metrics of the files diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 7329d59..47fa011 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -17,17 +17,17 @@ "gfastats", "gfastats/grTriPseu1.assembly_summary", "pipeline_info", - "pipeline_info/nf_core_pipeline_software_mqc_versions.yml" + "pipeline_info/ear_software_mqc_versions.yml" ], - 0, + 1, [ - + "grTriPseu1.assembly_summary:md5,49d6ad52839bf6597b0ff6fb9ff01151" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.04.4" }, - "timestamp": "2025-02-07T12:39:47.429262" + "timestamp": "2025-02-07T16:10:18.940156" } } \ No newline at end of file From b2c0c7da133f54f41642fbc22098bffc3e9f64fe Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 7 Feb 2025 16:52:21 +0000 Subject: [PATCH 11/20] Update snapshot --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index b1b6eeb..db0d1a3 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,6 +26,6 @@ params { // Input data for full size test // Limit resources so that this can run on GitHub Actions - input = "${baseDir}/assets/test-local.yaml" + input = "${baseDir}/assets/test.yaml" steps = "btk,cpretext,merquryfk" } From 2b2c7a5f2e16c0127fa2cf9f42cd5df1d5e9a113 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Mon, 10 Feb 2025 10:19:47 +0000 Subject: [PATCH 12/20] Updates --- conf/base.config | 2 +- conf/test.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/base.config b/conf/base.config index 4030c5e..dfefc57 100644 --- a/conf/base.config +++ b/conf/base.config @@ -26,7 +26,7 @@ process { withName: "MINIMAP2_ALIGN_SE" { cpus = { check_max( 16 ) } memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 60 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * task.attempt )) } - time = { check_max( 1.h * ( reference.size() < 1e9 ? 15 : reference.size() < 10e9 ? 30 : 48)) } + time = { check_max( 22.h * task.attempt, 'time' ) } } // Process-specific resource requirements diff --git a/conf/test.config b/conf/test.config index db0d1a3..cb0859c 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,6 +26,6 @@ params { // Input data for full size test // Limit resources so that this can run on GitHub Actions - input = "${baseDir}/assets/test.yaml" + input = "${baseDir}/assets/test.yaml" steps = "btk,cpretext,merquryfk" } From df978470fa95876d092b286063ad8d8a9d699e8c Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 12 Feb 2025 11:36:05 +0000 Subject: [PATCH 13/20] Updated to remove mapping --- CHANGELOG.md | 23 +++++ assets/test.yaml | 5 +- bin/generate_samplesheet.py | 18 ++-- conf/sanger-tol-btk.config | 7 -- conf/test_full.config | 9 +- modules/local/generate_samplesheet.nf | 3 +- modules/local/sanger_tol_btk.nf | 8 +- subworkflows/local/main_mapping.nf | 77 ----------------- subworkflows/local/pe_mapping.nf | 116 -------------------------- subworkflows/local/se_mapping.nf | 115 ------------------------- subworkflows/local/yaml_input.nf | 1 - workflows/ear.nf | 31 ++----- 12 files changed, 47 insertions(+), 366 deletions(-) delete mode 100644 conf/sanger-tol-btk.config delete mode 100644 subworkflows/local/main_mapping.nf delete mode 100644 subworkflows/local/pe_mapping.nf delete mode 100644 subworkflows/local/se_mapping.nf diff --git a/CHANGELOG.md b/CHANGELOG.md index f8847d1..591394f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,29 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). Naming based on: [Audiologists](https://en.wikipedia.org/wiki/Category:Audiologists). +## v0.7.0 - Raymond Carhart [12/02/2025] + - Removing the mapping subworkflow as it is no longer needed. + - This was a requirement before BLOBTOOLKIT implemented it's own mapping subworkflow. + - This significantly speeds up the pipeline in two ways. + - We no longer have to wait for mapping to complete prior to BTK. + - BTK doesn't have to struggle with the much larger mapped bam that was being created. + - NF-TEST implementation. + - We have implemented an output file sanity check rather than rely soley on pipeline completion. + +### Software dependencies +No Software updates + +### Parameters + +| Old parameter | New parameter | +| ------------- | ------------- | +| --mapped | | + +### KNOWN BUG +- BLOBTOOLKIT relies on BUSCO 5.5, which does NOT run with single line fasta! + - This needs to be folded, use `seqkit seq -l 70` + + ## v0.6.2 - Robert Beiny H2 [09/01/2025] - Modules have been updated to remove conda defaults. diff --git a/assets/test.yaml b/assets/test.yaml index 0f5f6ed..427144b 100755 --- a/assets/test.yaml +++ b/assets/test.yaml @@ -8,8 +8,8 @@ reference_haplotigs: /home/runner/work/ear/ear/TreeValTinyData/assembly/draft/gr mapped_bam: [] merquryfk: - fastk_hist: "./" - fastk_ktab: "./" + fastk_hist: "/home/runner/work/ear/ear/TreeValTinyData/genomic_data/pacbio/kmer.31/gfTriPseu1.50000.k31.hist" + fastk_ktab: "/home/runner/work/ear/ear/TreeValTinyData/genomic_data/pacbio/kmer.31/" # Used by both subpipelines longread: @@ -30,4 +30,3 @@ btk: diamond_nr_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd ncbi_taxonomy_path: /home/runner/work/ascc/ascc/ncbi_taxdump/ ncbi_rankedlineage_path: /home/runner/work/ascc/ascc/ncbi_taxdump/rankedlineage.dmp - config: /home/runner/work/ear/ear/conf/sanger-tol-btk.config diff --git a/bin/generate_samplesheet.py b/bin/generate_samplesheet.py index 12af705..6d4aacd 100755 --- a/bin/generate_samplesheet.py +++ b/bin/generate_samplesheet.py @@ -17,11 +17,12 @@ def parse_args(): parser = argparse.ArgumentParser(description="Generate a csv file for BTK") parser.add_argument("sample_name", type=str, help="Name of sample") parser.add_argument( - "mapped_bam_file", + "path_to_reads", type=str, - help="Path containing the mapped BAM generated with PacBio data and the ASCC input assembly", + help="Path containing the PacBio reads", ) - parser.add_argument("-v", "--version", action="version", version="1.0.0") + parser.add_argument("-v", "--version", action="version", version="1.1.0") + return parser.parse_args() @@ -31,10 +32,13 @@ def main(): data_list = [] data_list.append("sample,datatype,datafile\n") - if args.mapped_bam_file.endswith(".bam"): - data_list.append(f"{args.sample_name},pacbio,{args.mapped_bam_file}\n") - else: - sys.exit("I was expecting a mapped BAM file") + + [data_list.append(f"{args.sample_name},pacbio,{args.path_to_reads}{file}\n") for file in os.listdir(args.path_to_reads) if file.endswith('.fasta.gz')] + + print(data_list) + + if len(data_list) <= 1: + sys.exit("I was expecting at least one FASTA.GZ file") with open("samplesheet.csv", "w") as file: file.write("".join(data_list)) diff --git a/conf/sanger-tol-btk.config b/conf/sanger-tol-btk.config deleted file mode 100644 index 553ad56..0000000 --- a/conf/sanger-tol-btk.config +++ /dev/null @@ -1,7 +0,0 @@ -process { - withLabel:RUN_BLASTN:BLASTN_TAXON { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 10.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } - } -} diff --git a/conf/test_full.config b/conf/test_full.config index 8dee69b..5d5b23e 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -14,11 +14,6 @@ params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' - // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' - - // Fasta references - fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz' + input = "${projectDir}/assets/test-local.yaml" + outdir = "results" } diff --git a/modules/local/generate_samplesheet.nf b/modules/local/generate_samplesheet.nf index 018f7ec..e0e1b4a 100644 --- a/modules/local/generate_samplesheet.nf +++ b/modules/local/generate_samplesheet.nf @@ -8,7 +8,8 @@ process GENERATE_SAMPLESHEET { 'biocontainers/python:3.9' }" input: - tuple val(meta), path(pacbio_path) + tuple val(meta), path(reference) + val(pacbio_path) output: tuple val(meta), path("*csv"), emit: csv diff --git a/modules/local/sanger_tol_btk.nf b/modules/local/sanger_tol_btk.nf index 543e693..a50b005 100644 --- a/modules/local/sanger_tol_btk.nf +++ b/modules/local/sanger_tol_btk.nf @@ -4,12 +4,10 @@ process SANGER_TOL_BTK { input: tuple val(meta), path(reference, stageAs: "REFERENCE.fa") - tuple val(meta1), path(bam) // Name needs to remain the same as previous process as they are referenced in the samplesheet tuple val(meta2), path(samplesheet_csv, stageAs: "SAMPLESHEET.csv") path blastp, stageAs: "blastp.dmnd" path blastn path blastx - path config_file path tax_dump val busco_lineages val taxon @@ -32,7 +30,6 @@ process SANGER_TOL_BTK { def executor = task.ext.executor ?: "" def profiles = task.ext.profiles ?: "" def get_version = task.ext.version_data ?: "UNKNOWN - SETTING NOT SET" - def config = config_file ? "-c $config_file" : "" def pipeline_version = task.ext.version ?: "main" // Seems to be an issue where a nested pipeline can't see the files in the same directory @@ -61,9 +58,8 @@ process SANGER_TOL_BTK { --blastp "\$(realpath blastp.dmnd)" \\ --blastn "\$(realpath $blastn)" \\ --blastx "\$(realpath $blastx)" \\ - $config \\ - $args \\ - -resume' + --align + $args' cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/main_mapping.nf b/subworkflows/local/main_mapping.nf deleted file mode 100644 index 0531201..0000000 --- a/subworkflows/local/main_mapping.nf +++ /dev/null @@ -1,77 +0,0 @@ -include { SE_MAPPING } from './se_mapping' -include { PE_MAPPING } from './pe_mapping' - -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' - - -workflow MAIN_MAPPING { - - take: - sample_id // val(sample_id) - platform // val(data_type) - reference_hap1 // tuple val(meta), path(reference) - pacbio_tuple // tuple val(meta), path(longread_path) - - main: - ch_align_bam = Channel.empty() - ch_versions = Channel.empty() - - // - // LOGIC: SANGER-TOL/BLOBTOOLKIT expects the pacbio data to be already mapped -> this has been changed but seeing as BTK and genomenote need it then we may as well keep it. - // This is also a requirement for genomenote - // - - if ( platform.filter { it == "hifi" } || platform.filter { it == "clr" } || platform.filter { it == "ont" } ) { - // - // SUBWORKFLOW: SINGLE END MAPPING FOR ALIGNING LONGREAD DATA - // - SE_MAPPING ( - reference_hap1, - pacbio_tuple, - platform - ) - ch_versions = ch_versions.mix(SE_MAPPING.out.versions) - - ch_align_bam - .mix( SE_MAPPING.out.mapped_bam ) - .set { merged_bam } - } - else if ( platform.filter { it == "illumina" } ) { - // - // SUBWORKFLOW: PAIRED END MAPPING FOR ALIGNING LONGREAD DATA - // - PE_MAPPING ( - reference_hap1, - pacbio_tuple, - platform - ) - ch_versions = ch_versions.mix(PE_MAPPING.out.versions) - - ch_align_bam - .mix( PE_MAPPING.out.mapped_bam ) - .set { merged_bam } - } - - // - // MODULE: SORT MAPPED BAM - // - SAMTOOLS_SORT ( - merged_bam, - reference_hap1 - ) - ch_versions = ch_versions.mix( SAMTOOLS_SORT.out.versions ) - - sample_id - .combine(merged_bam) - .map{ sample_id, pacbio_meta, pacbio_path -> - tuple( [id: sample_id], - pacbio_path - ) - } - .set { mapped_bam } - - emit: - mapped_bam // channel: tuple val(meta), path(mapped_bam) - versions = ch_versions // channel: [ path(versions.yml) ] - -} diff --git a/subworkflows/local/pe_mapping.nf b/subworkflows/local/pe_mapping.nf deleted file mode 100644 index 358be3b..0000000 --- a/subworkflows/local/pe_mapping.nf +++ /dev/null @@ -1,116 +0,0 @@ -include { MINIMAP2_ALIGN as MINIMAP2_ALIGN_ILLUMINA } from '../../modules/nf-core/minimap2/align/main' -include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main' - -workflow PE_MAPPING { - - take: - reference_tuple // Channel [ val(meta), path(file) ] - pacbio_tuple // Channel [ val(meta), val( str ) ] - reads_type // Channel val( str ) - - main: - ch_versions = Channel.empty() - - - // - // PROCESS: GETS PACBIO READ PATHS FROM READS_PATH - // - ch_grabbed_reads_path = GrabFiles( pacbio_tuple ) - - ch_grabbed_reads_path - .map { meta, files -> - tuple( files ) - } - .flatten() - .set { ch_reads_path } - - // - // PROCESS: MAKE MINIMAP INPUT CHANNEL - // - reference_tuple - .combine( ch_reads_path ) - .combine( reads_type ) - .map { meta, ref, reads_path, reads_type -> - tuple( - [ id : meta.id, - single_end : false, - readtype: reads_type.toString() - ], - reads_path, - ref, - true, - false, - false, - reads_type - ) - } - .set { pe_input } - - // - // PROCESS: MULTIMAP TO MAKE BOOLEAN ARGUMENTS - // - pe_input - .multiMap { meta, reads_path, ref, bam_output, cigar_paf, cigar_bam, reads_type -> - read_tuple : tuple( meta, read_path) - ref : ref - bool_bam_ouput : bam_output - bool_cigar_paf : cigar_paf - bool_cigar_bam : cigar_bam - } - .set { illumina_input } - - // - // MODULE: PAIRED END READ MAPPING USING MINIMAP - // - MINIMAP2_ALIGN_ILLUMINA ( - illumina_input.read_tuple, - illumina_input.ref, - illumina_input.bool_bam_ouput, - [], - illumina_input.bool_cigar_paf, - illumina_input.bool_cigar_bam - ) - ch_versions = ch_versions.mix(MINIMAP2_ALIGN_ILLUMINA.out.versions) - - ch_bams = MINIMAP2_ALIGN_ILLUMINA.out.bam - - ch_bams - .map { meta, file -> - tuple( file ) - } - .collect() - .map { file -> - tuple ( - [ id : file[0].toString().split('/')[-1].split('_')[0] ], // Change sample ID - file - ) - } - .set { collected_files_for_merge } - - // - // MODULE: MERGE ALL OUTPUT BAM - // - SAMTOOLS_MERGE( - collected_files_for_merge, - reference_tuple, - [[],[]] - ) - ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) - - emit: - versions = ch_versions.ifEmpty(null) - mapped_bam = SAMTOOLS_MERGE.out.bam -} - -process GrabFiles { - tag "${meta.id}" - executor 'local' - - input: - tuple val(meta), path("in") - - output: - tuple val(meta), path("in/*.{fa,fasta}.{gz}") - - "true" -} diff --git a/subworkflows/local/se_mapping.nf b/subworkflows/local/se_mapping.nf deleted file mode 100644 index c3307d4..0000000 --- a/subworkflows/local/se_mapping.nf +++ /dev/null @@ -1,115 +0,0 @@ -include { MINIMAP2_ALIGN as MINIMAP2_ALIGN_SE } from '../../modules/nf-core/minimap2/align/main' -include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main' - -workflow SE_MAPPING { - - take: - reference_tuple // Channel [ val(meta), path(file) ] - pacbio_tuple // Channel [ val(meta), path(file) ] - reads_type // Channel val( str ) - - main: - ch_versions = Channel.empty() - ch_align_bams = Channel.empty() - - // - // PROCESS: GETS PACBIO READ PATHS FROM READS_PATH - // - ch_grabbed_reads_path = GrabFiles(pacbio_tuple) - - ch_grabbed_reads_path - .map {meta, files -> - tuple(files) - } - .flatten() - .set {ch_reads_path} - - // - // PROCESS: MAKE MINIMAP INPUT CHANNEL AND MAKE BRANCHES BASED ON INPUT READ TYPE - // - ch_reads_path - .combine( reference_tuple ) - .combine( reads_type ) - .map { reads_path, meta, ref, reads_type -> - tuple( - [ id : meta.id, - single_end : true, - readtype : reads_type.toString() - ], - reads_path, - ref, - true, - false, - false, - reads_type - ) - } - .set {minimap_se_input} - - // - // PROCESS: MULTIMAP TO MAKE BOOLEAN ARGUMENTS FOR MINIMAP HIFI MAPPING INPUT - // - minimap_se_input - .multiMap { meta, reads_path, ref, bam_output, cigar_paf, cigar_bam, reads_type -> - read_tuple : tuple( meta, reads_path) - ref : tuple( meta, ref) - bool_bam_ouput : bam_output - bool_cigar_paf : cigar_paf - bool_cigar_bam : cigar_bam - } - .set { se_input } - - // - // MOUDLES: MAPPING DIFFERENT TYPE OF READ AGAINIST REFERENCE - // - - MINIMAP2_ALIGN_SE ( - se_input.read_tuple, - se_input.ref, - se_input.bool_bam_ouput, - [], - se_input.bool_cigar_paf, - se_input.bool_cigar_bam - ) - ch_bams = MINIMAP2_ALIGN_SE.out.bam - - ch_bams - .map { meta, file -> - tuple( file ) - } - .collect() - .map { file -> - tuple ( - [ id : file[0].toString().split('/')[-1].split('_')[0] ], // Change sample ID - file - ) - } - .set { collected_files_for_merge } - - // - // MODULE: MERGE ALL OUTPUT BAM - // - SAMTOOLS_MERGE( - collected_files_for_merge, - reference_tuple, - [[],[]] - ) - ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) - - emit: - versions = ch_versions.ifEmpty(null) - mapped_bam = SAMTOOLS_MERGE.out.bam -} - -process GrabFiles { - tag "${meta.id}" - executor 'local' - - input: - tuple val(meta), path("in") - - output: - tuple val(meta), path("in/*.{fa,fasta,fna}.{gz}") - - "true" -} diff --git a/subworkflows/local/yaml_input.nf b/subworkflows/local/yaml_input.nf index 4e3cc9e..fd9019e 100644 --- a/subworkflows/local/yaml_input.nf +++ b/subworkflows/local/yaml_input.nf @@ -114,7 +114,6 @@ workflow YAML_INPUT { btk_taxid = Channel.of(inputs.btk.taxid) btk_gca_accession = Channel.of(inputs.btk.gca_accession) busco_lineages = Channel.of(inputs.btk.lineages) - btk_config = Channel.fromPath(inputs.btk.config) versions = ch_versions.ifEmpty(null) } diff --git a/workflows/ear.nf b/workflows/ear.nf index a37966c..600fd65 100644 --- a/workflows/ear.nf +++ b/workflows/ear.nf @@ -10,7 +10,6 @@ include { SANGER_TOL_CPRETEXT } from '../modules/local/sanger_tol_ // Subworkflow imports include { YAML_INPUT } from '../subworkflows/local/yaml_input' -include { MAIN_MAPPING } from '../subworkflows/local/main_mapping' // Module imports include { CAT_CAT } from '../modules/nf-core/cat/cat/main' @@ -66,7 +65,9 @@ workflow EAR { .map{ sample_id, file1, file2 -> tuple( [ id: sample_id ], - [file1, file2] + [ file1, + file2 + ] ) } .set { @@ -132,27 +133,6 @@ workflow EAR { ch_versions = ch_versions.mix( MERQURYFK_MERQURYFK.out.versions ) } - // - // LOGIC: IF A MAPPED BAM FILE EXISTS AND THE FLAG `mapped` IS TRUE - // SKIP THE MAPPING SUBWORKFLOW - // - if (!params.mapped) { - // - // SUBWORKFLOW: MAIN_MAPPING CONTAINS ALL THE MAPPING LOGIC - // This allows us to more esily bypass the mapping if we already have a sorted and mapped bam - // - MAIN_MAPPING ( - YAML_INPUT.out.sample_id, - YAML_INPUT.out.longread_type, - YAML_INPUT.out.reference_hap1, - YAML_INPUT.out.pacbio_tuple, - ) - ch_versions = ch_versions.mix( MAIN_MAPPING.out.versions ) - ch_mapped_bam = MAIN_MAPPING.out.mapped_bam - } else { - ch_mapped_bam = YAML_INPUT.out.mapped_bam - } - // // LOGIC: STEP TO STOP BTK RUNNING IF SPECIFIED BY USER @@ -163,7 +143,8 @@ workflow EAR { // MODULE: GENERATE_SAMPLESHEET creates a csv for the blobtoolkit pipeline // GENERATE_SAMPLESHEET( - ch_mapped_bam + YAML_INPUT.out.reference_hap1, + YAML_INPUT.out.longread_dir ) ch_versions = ch_versions.mix( GENERATE_SAMPLESHEET.out.versions ) @@ -173,12 +154,10 @@ workflow EAR { // SANGER_TOL_BTK ( YAML_INPUT.out.reference_hap1, - ch_mapped_bam, GENERATE_SAMPLESHEET.out.csv, YAML_INPUT.out.btk_un_diamond_database, YAML_INPUT.out.btk_nt_database, YAML_INPUT.out.btk_un_diamond_database, - YAML_INPUT.out.btk_config, YAML_INPUT.out.btk_ncbi_taxonomy_path, YAML_INPUT.out.busco_lineages, YAML_INPUT.out.btk_taxid, From e03814bd2ccacf05b50b723271c5a0dbb2fd5d27 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 12 Feb 2025 13:44:06 +0000 Subject: [PATCH 14/20] Removing unused vbase.config --- bin/generate_samplesheet.py | 2 -- conf/base.config | 6 ------ modules/local/sanger_tol_btk.nf | 15 ++++++++------- 3 files changed, 8 insertions(+), 15 deletions(-) diff --git a/bin/generate_samplesheet.py b/bin/generate_samplesheet.py index 6d4aacd..690adc6 100755 --- a/bin/generate_samplesheet.py +++ b/bin/generate_samplesheet.py @@ -35,8 +35,6 @@ def main(): [data_list.append(f"{args.sample_name},pacbio,{args.path_to_reads}{file}\n") for file in os.listdir(args.path_to_reads) if file.endswith('.fasta.gz')] - print(data_list) - if len(data_list) <= 1: sys.exit("I was expecting at least one FASTA.GZ file") diff --git a/conf/base.config b/conf/base.config index 4b330f4..e07e4a3 100644 --- a/conf/base.config +++ b/conf/base.config @@ -23,12 +23,6 @@ process { time = { check_max( 70.h * task.attempt, 'time' ) } } - withName: "MINIMAP2_ALIGN_SE" { - cpus = { check_max( 16 , 'cpus' ) } - memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 60 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * task.attempt ) , 'memory') } - time = { check_max( 1.h * ( reference.size() < 1e9 ? 15 : reference.size() < 10e9 ? 30 : 48), 'time' ) } - } - // Process-specific resource requirements // NOTE - Please try and re-use the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. diff --git a/modules/local/sanger_tol_btk.nf b/modules/local/sanger_tol_btk.nf index a50b005..f8d688a 100644 --- a/modules/local/sanger_tol_btk.nf +++ b/modules/local/sanger_tol_btk.nf @@ -14,13 +14,13 @@ process SANGER_TOL_BTK { val gca_accession output: - tuple val(meta), path("*_out/blobtoolkit/REFERENCE"), emit: dataset - path "*_out/blobtoolkit/plots" , emit: plots - path "*_out/blobtoolkit/REFERENCE/summary.json.gz", emit: summary_json - path "*_out/busco", emit: busco_data - path "*_out/multiqc", emit: multiqc_report - path "*_out/pipeline_info/blobtoolkit", emit: pipeline_info - path "versions.yml", emit: versions + tuple val(meta), path("*_out/blobtoolkit/REFERENCE"), emit: dataset + path "*_out/blobtoolkit/plots" , emit: plots + path "*_out/blobtoolkit/REFERENCE/summary.json.gz", emit: summary_json + path "*_out/busco", emit: busco_data + path "*_out/multiqc", emit: multiqc_report + path "*_out/pipeline_info/blobtoolkit", emit: pipeline_info + path "*out/pipeline_info/blobtoolkit/software_versions.yml", emit: versions script: def pipeline_name = task.ext.pipeline_name @@ -58,6 +58,7 @@ process SANGER_TOL_BTK { --blastp "\$(realpath blastp.dmnd)" \\ --blastn "\$(realpath $blastn)" \\ --blastx "\$(realpath $blastx)" \\ + --use_work_dir_as_temp true \\ --align $args' From 18f68f980bedfe7925dcda2b919bab39841b6ad0 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 12 Feb 2025 13:56:30 +0000 Subject: [PATCH 15/20] Updates to md files --- CHANGELOG.md | 18 ++++++++++-------- nextflow.config | 14 +++++++------- 2 files changed, 17 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 591394f..c0d3f2a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,15 +5,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 Naming based on: [Audiologists](https://en.wikipedia.org/wiki/Category:Audiologists). ## v0.7.0 - Raymond Carhart [12/02/2025] - - Removing the mapping subworkflow as it is no longer needed. - - This was a requirement before BLOBTOOLKIT implemented it's own mapping subworkflow. - - This significantly speeds up the pipeline in two ways. - - We no longer have to wait for mapping to complete prior to BTK. - - BTK doesn't have to struggle with the much larger mapped bam that was being created. - - NF-TEST implementation. - - We have implemented an output file sanity check rather than rely soley on pipeline completion. + +- Removing the mapping subworkflow as it is no longer needed. + - This was a requirement before BLOBTOOLKIT implemented it's own mapping subworkflow. + - This significantly speeds up the pipeline in two ways. + - We no longer have to wait for mapping to complete prior to BTK. + - BTK doesn't have to struggle with the much larger mapped bam that was being created. +- NF-TEST implementation. + - We have implemented an output file sanity check rather than rely soley on pipeline completion. ### Software dependencies + No Software updates ### Parameters @@ -23,10 +25,10 @@ No Software updates | --mapped | | ### KNOWN BUG + - BLOBTOOLKIT relies on BUSCO 5.5, which does NOT run with single line fasta! - This needs to be folded, use `seqkit seq -l 70` - ## v0.6.2 - Robert Beiny H2 [09/01/2025] - Modules have been updated to remove conda defaults. diff --git a/nextflow.config b/nextflow.config index 8202943..451a676 100644 --- a/nextflow.config +++ b/nextflow.config @@ -219,12 +219,12 @@ manifest { contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ - name: 'DLBPointon', - affiliation: '', - email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') - orcid: '' + name: 'Damon-Lee B Pointon', + affiliation: 'Wellcome Genome Campus, Sanger', + email: 'dp24@sanger.ac.uk', + github: 'DLBPointon', + contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0003-2949-6719' ], ] homePage = 'https://github.com/sanger-tol/ear' @@ -232,7 +232,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=24.04.2' - version = '0.6.2' + version = '0.7.0' doi = 'https://zenodo.org/records/13819520' } From c18a84a1625e07a3e70b45d264569c4b686c2704 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 12 Feb 2025 14:52:14 +0000 Subject: [PATCH 16/20] Updates to the CICD --- .github/workflows/ci.yml | 6 +++++ assets/test-local.yaml | 7 ++---- assets/test.yaml | 4 ++-- conf/test.config | 2 +- conf/test_full.config | 1 + nf-test.config | 2 +- tests/main.nf.test | 12 ++++++---- tests/main.nf.test.snap | 52 ++++++++++++++++++++++++++++++++++++---- 8 files changed, 69 insertions(+), 17 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7dc79ab..f843489 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -62,6 +62,12 @@ jobs: cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-hap.fa cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa + - name: Download EAR MerquryFK data + # Generated .hist and .ktab files (+ hidden files) that is required to test merquryfk + run: | + curl https://tolit.cog.sanger.ac.uk/test-data/resources/ear/EAR_merquryfk_input.tar.gz | tar xzf - + mv EAR_merquryfk_input TreeValTinyData/genomic_data/pacbio/ + - name: Install nf-test uses: nf-core/setup-nf-test@v1 diff --git a/assets/test-local.yaml b/assets/test-local.yaml index c5e9ab5..2475de6 100755 --- a/assets/test-local.yaml +++ b/assets/test-local.yaml @@ -4,12 +4,9 @@ reference_hap1: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/ass reference_hap2: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-hap.fa reference_haplotigs: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa -# If a mapped bam already exists use the below + --mapped TRUE on the nextflow command else ignore. -mapped_bam: [] - merquryfk: - fastk_hist: "./EMPTY.hist" - fastk_ktab: "./EMPTY.ktab" + fastk_hist: "/nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/genomic_data/pacbio/kmer.31/gfTriPseu1.50000.k31.hist" + fastk_ktab: "/nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/genomic_data/pacbio/kmer.31/" # Used by both subpipelines longread: diff --git a/assets/test.yaml b/assets/test.yaml index 21d5767..bd048b3 100755 --- a/assets/test.yaml +++ b/assets/test.yaml @@ -8,8 +8,8 @@ reference_haplotigs: /home/runner/work/ear/ear/TreeValTinyData/assembly/draft/gr mapped_bam: [] merquryfk: - fastk_hist: "./EMPTY.hist" - fastk_ktab: "./EMPTY.ktab" + fastk_hist: "/home/runner/work/ear/ear/TreeValTinyData/genomic_data/pacbio/EAR_merquryfk_input/gfTriPseu1.50000.k31.hist" + fastk_ktab: "/home/runner/work/ear/ear/TreeValTinyData/genomic_data/pacbio/EAR_merquryfk_input/" # Used by both subpipelines longread: diff --git a/conf/test.config b/conf/test.config index cb0859c..907bda8 100644 --- a/conf/test.config +++ b/conf/test.config @@ -27,5 +27,5 @@ params { // Input data for full size test // Limit resources so that this can run on GitHub Actions input = "${baseDir}/assets/test.yaml" - steps = "btk,cpretext,merquryfk" + steps = "btk,cpretext" } diff --git a/conf/test_full.config b/conf/test_full.config index 5d5b23e..ac2f087 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,4 +16,5 @@ params { input = "${projectDir}/assets/test-local.yaml" outdir = "results" + steps = "btk,cpretext" } diff --git a/nf-test.config b/nf-test.config index cc4372f..5091d8c 100644 --- a/nf-test.config +++ b/nf-test.config @@ -11,6 +11,6 @@ config { load "nft-utils@0.0.3" } - configFile "conf/test.config" + configFile "conf/test_full.config" profile "test" } diff --git a/tests/main.nf.test b/tests/main.nf.test index f3002ca..716ad42 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_pipeline { def gfastats = getAllFilesFromDir(params.outdir, include: ['gfastats/*_summary']) - //def merquryfk = getAllFilesFromDir(params.outdir, include: ['merquryfk/*']) + def merquryfk = getAllFilesFromDir(params.outdir, include: ['merquryfk/*']) assertAll ( {assert workflow.success}, @@ -38,9 +38,13 @@ nextflow_pipeline { gfastats, // MERQURY_FK is running statistics on the input files - // input files are also split between the two main input haps - // need to actually test merqury first - //merquryfk, + merquryfk.size(), + merquryfk, + merquryfk.any{it.toString().contains("combined_haplos".toString())}, + merquryfk.any{it.toString().contains("spectra".toString())}, + merquryfk.any{it.toString().contains(".qv".toString())}, + merquryfk.any{it.toString().contains(".bed".toString())}, + merquryfk.any{it.toString().contains(".stats".toString())} ).match()}, ) diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 47fa011..f890d51 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -1,7 +1,7 @@ { "Minimal run | No SANGER-TOL-* nested pipelines": { "content": [ - 2, + 3, { "CAT_CAT": { "pigz": "2.3.4" @@ -9,25 +9,69 @@ "GFASTATS": { "gfastats": "1.3.6" }, + "MERQURYFK_MERQURYFK": { + "fastk": "f18a4e6d2207539f7b84461daebc54530a9559b0", + "merquryfk": "8ae344092df5dcaf83cfb7f90f662597a9b1fc61", + "r": "4.2.0" + }, "Workflow": { - "sanger-tol/ear": "v0.6.2" + "sanger-tol/ear": "v0.7.0" } }, [ "gfastats", "gfastats/grTriPseu1.assembly_summary", + "merquryfk", + "merquryfk/grTriPseu1.combined_haplos.qv", + "merquryfk/grTriPseu1.combined_haplos.spectra-cn.fl.png", + "merquryfk/grTriPseu1.combined_haplos.spectra-cn.ln.png", + "merquryfk/grTriPseu1.combined_haplos.spectra-cn.st.png", + "merquryfk/grTriPseu1.combined_haplos_only.bed", + "merquryfk/grTriPseu1.completeness.stats", + "merquryfk/grTriPseu1.grTriPseu1.qv", + "merquryfk/grTriPseu1.grTriPseu1.spectra-cn.fl.png", + "merquryfk/grTriPseu1.grTriPseu1.spectra-cn.ln.png", + "merquryfk/grTriPseu1.grTriPseu1.spectra-cn.st.png", + "merquryfk/grTriPseu1.grTriPseu1_only.bed", + "merquryfk/grTriPseu1.qv", + "merquryfk/grTriPseu1.spectra-asm.fl.png", + "merquryfk/grTriPseu1.spectra-asm.ln.png", + "merquryfk/grTriPseu1.spectra-asm.st.png", "pipeline_info", "pipeline_info/ear_software_mqc_versions.yml" ], 1, [ "grTriPseu1.assembly_summary:md5,49d6ad52839bf6597b0ff6fb9ff01151" - ] + ], + 15, + [ + "grTriPseu1.combined_haplos.qv:md5,ee9ad1aea0ad003e5ac866df174902f1", + "grTriPseu1.combined_haplos.spectra-cn.fl.png:md5,50bad6b85b8f80b8411b50e4119bc959", + "grTriPseu1.combined_haplos.spectra-cn.ln.png:md5,50bad6b85b8f80b8411b50e4119bc959", + "grTriPseu1.combined_haplos.spectra-cn.st.png:md5,50bad6b85b8f80b8411b50e4119bc959", + "grTriPseu1.combined_haplos_only.bed:md5,04220c269d33e2bbc1122595828d8275", + "grTriPseu1.completeness.stats:md5,a3d2d772cc118547335dde59161b9217", + "grTriPseu1.grTriPseu1.qv:md5,953ba4f3322475292919671a2393b52d", + "grTriPseu1.grTriPseu1.spectra-cn.fl.png:md5,4b0c20fb8c99b0e725d569fc7252078f", + "grTriPseu1.grTriPseu1.spectra-cn.ln.png:md5,7f07db43d617056109c2ebab5b47b7cc", + "grTriPseu1.grTriPseu1.spectra-cn.st.png:md5,9717069c33da319c45f0d976b3697b66", + "grTriPseu1.grTriPseu1_only.bed:md5,9af876714b7666bb628a21dd275d0691", + "grTriPseu1.qv:md5,0d51bda46c4cafbeb3c082768beefd6b", + "grTriPseu1.spectra-asm.fl.png:md5,50bad6b85b8f80b8411b50e4119bc959", + "grTriPseu1.spectra-asm.ln.png:md5,50bad6b85b8f80b8411b50e4119bc959", + "grTriPseu1.spectra-asm.st.png:md5,50bad6b85b8f80b8411b50e4119bc959" + ], + true, + true, + true, + true, + true ], "meta": { "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2025-02-07T16:10:18.940156" + "timestamp": "2025-02-12T14:49:22.178822" } } \ No newline at end of file From 239ea63ae076341ded53e09686977b1d1393fac3 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 12 Feb 2025 14:58:59 +0000 Subject: [PATCH 17/20] Updates to the CICD --- nf-test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-test.config b/nf-test.config index 5091d8c..cc4372f 100644 --- a/nf-test.config +++ b/nf-test.config @@ -11,6 +11,6 @@ config { load "nft-utils@0.0.3" } - configFile "conf/test_full.config" + configFile "conf/test.config" profile "test" } From 17d48360ebd01608f6a07c1e9f5b9140111b1e2a Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 13 Feb 2025 10:09:59 +0000 Subject: [PATCH 18/20] minor changes --- conf/base.config | 2 +- nextflow.config | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 3f4f55a..a29e1cd 100644 --- a/conf/base.config +++ b/conf/base.config @@ -20,7 +20,7 @@ process { maxErrors = '-1' withName: "SANGER_TOL_CPRETEXT|SANGER_TOL_BTK" { - time = { check_max( 70.h * task.attempt) } + time = { check_max( 70.h * task.attempt, 'time') } } // Process-specific resource requirements diff --git a/nextflow.config b/nextflow.config index 451a676..cf1f9ce 100644 --- a/nextflow.config +++ b/nextflow.config @@ -276,3 +276,39 @@ def readWithDefault( String path, Object default_channel ) { def resolveFileFromDir ( String path, Object dir ){ dir.map{ results -> file( results.resolve( path ) ) } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + +// Function to ensure that resource requirements don't go beyond +// a maximum limit +def check_max(obj, type) { + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'time') { + try { + if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) + return params.max_time as nextflow.util.Duration + else + return obj + } catch (all) { + println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'cpus') { + try { + return Math.min( obj, params.max_cpus as int ) + } catch (all) { + println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" + return obj + } + } +} From d26b96507747446fe4324d23aba0c2fc00479146 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Mon, 17 Feb 2025 10:26:51 +0000 Subject: [PATCH 19/20] Re-adding check_max --- conf/base.config | 2 +- nextflow.config | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 3f4f55a..a29e1cd 100644 --- a/conf/base.config +++ b/conf/base.config @@ -20,7 +20,7 @@ process { maxErrors = '-1' withName: "SANGER_TOL_CPRETEXT|SANGER_TOL_BTK" { - time = { check_max( 70.h * task.attempt) } + time = { check_max( 70.h * task.attempt, 'time') } } // Process-specific resource requirements diff --git a/nextflow.config b/nextflow.config index 451a676..7dcc04a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -276,3 +276,36 @@ def readWithDefault( String path, Object default_channel ) { def resolveFileFromDir ( String path, Object dir ){ dir.map{ results -> file( results.resolve( path ) ) } } + +// Function to ensure that resource requirements don't go beyond +// a maximum limit +def check_max(obj, type) { + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'time') { + try { + if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) + return params.max_time as nextflow.util.Duration + else + return obj + } catch (all) { + println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'cpus') { + try { + return Math.min( obj, params.max_cpus as int ) + } catch (all) { + println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" + return obj + } + } +} From 4a6f5442a8d4da538b317bdc58901ab7ab9985bd Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 19 Feb 2025 12:40:47 +0000 Subject: [PATCH 20/20] moving around the -resume flag --- conf/modules.config | 6 +++--- modules/local/sanger_tol_btk.nf | 3 +-- modules/local/sanger_tol_cpretext.nf | 3 +-- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index ac33898..03667b1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -38,7 +38,7 @@ process { withName: SANGER_TOL_BTK { ext.pipeline_name = "sanger-tol/blobtoolkit" - ext.args = "" + ext.args = "-resume" ext.executor = "bsub -Is -tty -e test.e -o test.log -n 2 -q oversubscribed -M1400 -R'select[mem>1400] rusage[mem=1400] span[hosts=1]'" ext.profiles = "singularity,sanger" ext.get_versions = "lsid | head -n1 | cut -d ',' -f 1" @@ -47,11 +47,11 @@ process { withName: SANGER_TOL_CPRETEXT { ext.pipeline_name = "sanger-tol/curationpretext" - ext.args = "" + ext.args = "-resume" ext.executor = "bsub -Is -tty -e test.e -o test.log -n 2 -q oversubscribed -M1400 -R'select[mem>1400] rusage[mem=1400] span[hosts=1]'" ext.profiles = "singularity,sanger" ext.get_versions = "lsid | head -n1 | cut -d ',' -f 1" - ext.version = "1.1.0" + ext.version = "dev" } } diff --git a/modules/local/sanger_tol_btk.nf b/modules/local/sanger_tol_btk.nf index 543e693..dc2bbab 100644 --- a/modules/local/sanger_tol_btk.nf +++ b/modules/local/sanger_tol_btk.nf @@ -62,8 +62,7 @@ process SANGER_TOL_BTK { --blastn "\$(realpath $blastn)" \\ --blastx "\$(realpath $blastx)" \\ $config \\ - $args \\ - -resume' + $args' cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/sanger_tol_cpretext.nf b/modules/local/sanger_tol_cpretext.nf index b073039..c1c58a1 100644 --- a/modules/local/sanger_tol_cpretext.nf +++ b/modules/local/sanger_tol_cpretext.nf @@ -42,9 +42,8 @@ process SANGER_TOL_CPRETEXT { --outdir $output_dir \\ --longread "\$(realpath $longread_dir)" \\ --cram "\$(realpath $cram_dir)" \\ - $args \\ $config \\ - -resume' + $args' cat <<-END_VERSIONS > versions.yml "${task.process}":