diff --git a/modules.json b/modules.json index 6f57601..c43247b 100644 --- a/modules.json +++ b/modules.json @@ -154,12 +154,12 @@ }, "umitools/dedup": { "branch": "master", - "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "umitools/extract": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"], "patch": "modules/nf-core/umitools/extract/umitools-extract.diff" } diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml new file mode 100644 index 0000000..f443735 --- /dev/null +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -0,0 +1,7 @@ +name: umitools_dedup +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::umi_tools=1.1.4 diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 56ea046..5e48704 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -2,7 +2,7 @@ process UMITOOLS_DEDUP { tag "$meta.id" label "process_medium" - conda "bioconda::umi_tools=1.1.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' : 'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }" diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml index 534d4c6..38d3fd4 100644 --- a/modules/nf-core/umitools/dedup/meta.yml +++ b/modules/nf-core/umitools/dedup/meta.yml @@ -7,8 +7,8 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) - and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] input: @@ -61,8 +61,11 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" - "@klkeys" +maintainers: + - "@drpatelh" + - "@grst" + - "@klkeys" diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml new file mode 100644 index 0000000..7d08ac0 --- /dev/null +++ b/modules/nf-core/umitools/extract/environment.yml @@ -0,0 +1,7 @@ +name: umitools_extract +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::umi_tools=1.1.4 diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 77d7435..e61d476 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -3,7 +3,7 @@ process UMITOOLS_EXTRACT { label "process_single" label "process_long" - conda "bioconda::umi_tools=1.1.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.4--py38hbff2b2d_1' : 'biocontainers/umi_tools:1.1.4--py38hbff2b2d_1' }" diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml index db64a0f..7695b27 100644 --- a/modules/nf-core/umitools/extract/meta.yml +++ b/modules/nf-core/umitools/extract/meta.yml @@ -1,15 +1,16 @@ name: umitools_extract description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place keywords: - - umitools + - UMI + - barcode - extract + - umitools tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) - and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ - license: ["MIT"] + license: "MIT" input: - meta: type: map @@ -29,9 +30,7 @@ output: - reads: type: file description: > - Extracted FASTQ files. | - For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | - For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. pattern: "*.{fastq.gz}" - log: type: file @@ -41,7 +40,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test new file mode 100644 index 0000000..22242d1 --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/main.nf.test @@ -0,0 +1,35 @@ +nextflow_process { + + name "Test Process UMITOOLS_EXTRACT" + script "../main.nf" + process "UMITOOLS_EXTRACT" + config "./nextflow.config" + tag "modules_nfcore" + tag "modules" + tag "umitools" + tag "umitools/extract" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } +} \ No newline at end of file diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test.snap b/modules/nf-core/umitools/extract/tests/main.nf.test.snap new file mode 100644 index 0000000..54e77fb --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,866a2da05ce1af35cc07261ffe6bc31a" + ] + ], + "timestamp": "2023-10-17T08:25:55.427194" + } +} \ No newline at end of file diff --git a/modules/nf-core/umitools/extract/tests/nextflow.config b/modules/nf-core/umitools/extract/tests/nextflow.config new file mode 100644 index 0000000..c866f5a --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: UMITOOLS_EXTRACT { + ext.args = '--bc-pattern="NNNN"' + } + +} diff --git a/modules/nf-core/umitools/extract/tests/tags.yml b/modules/nf-core/umitools/extract/tests/tags.yml new file mode 100644 index 0000000..c3fb23d --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/tags.yml @@ -0,0 +1,2 @@ +umitools/extract: + - modules/nf-core/umitools/extract/**