Refactor variant prediction #268

jonasscheid · 2025-02-03T07:42:06Z

The last part of major refactoring #205:

Refactored and removed unused code in epaa.py (which generates peptides from variants (vcf input). EPYTOPE_VARIANT_PREDICTION only performs this task now. In previous versions the pipeline wrapped nextflow around this script, which inherently is not modular and extendable.
Removed not needed params
Adjusted and checked that all tests passed (locally).

PR checklist

…_prediction

…_output flag

…mouse has also two classes. Needs to be adjusted in nf-core test data

nf-core-bot · 2025-02-03T07:42:41Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2025-02-03T07:43:39Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 5781a91

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

nextflow_config - Config default value incorrect: params.max_peptide_length_classI is set as 14 in nextflow_schema.json but is 12 in nextflow.config.

❗ Test warnings:

schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/nf-core-epitopeprediction_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-epitopeprediction_logo_dark.png

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
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files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
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files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-epitopeprediction_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-epitopeprediction_logo_light.png
files_exist - File found: docs/images/nf-core-epitopeprediction_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
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files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
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files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-epitopeprediction_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowEpitopeprediction.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 2.4.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.genome_reference= grch37
nextflow_config - Config default value correct: params.peptide_col_name= sequence
nextflow_config - Config default value correct: params.min_peptide_length_classI= 8
nextflow_config - Config default value correct: params.min_peptide_length_classII= 8
nextflow_config - Config default value correct: params.max_peptide_length_classII= 25
nextflow_config - Config default value correct: params.tools= mhcflurry
nextflow_config - Config default value correct: params.fasta_output= false
nextflow_config - Config default value correct: params.wide_format_output= false
nextflow_config - Config default value correct: params.split_by_variants_size= 0
nextflow_config - Config default value correct: params.split_by_variants_distance= 110000
nextflow_config - Config default value correct: params.peptides_split_maxchunks= 100
nextflow_config - Config default value correct: params.peptides_split_minchunksize= 5000
nextflow_config - Config default value correct: params.netmhc_system= linux
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: ci-external.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - GUNZIP_VCF found in conf/modules.config and Nextflow scripts.
modules_config - VARIANT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - SNPSIFT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - EPYTOPE_VARIANT_PREDICTION found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - FASTA2PEPTIDES found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_PEPTIDES found in conf/modules.config and Nextflow scripts.
modules_config - PREPARE_PREDICTION_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - MHCFLURRY found in conf/modules.config and Nextflow scripts.
modules_config - MHCNUGGETS found in conf/modules.config and Nextflow scripts.
modules_config - NETMHCPAN found in conf/modules.config and Nextflow scripts.
modules_config - NETMHCIIPAN found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_PREDICTIONS found in conf/modules.config and Nextflow scripts.
modules_config - CSVTK_CONCAT found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2025-02-03 07:43:21

jonasscheid added 18 commits January 31, 2025 14:40

rename epytope_peptide_prediction to more appropriate epytope_variant…

ff5046c

…_prediction

drop use_affinity_thresholds param

d86bb10

Major refactor of generate peptides from variants script (epaa)

9e1fc68

Chain variant prediction channel with mhc-binding-subworkflow

7f3b4ee

use nf-core snpsift split instead of local module

d68cd9c

remove outdated modules

ff5fc3e

variant split module: file to folder

6fa21c5

add snpsift split nf-core module

58a6a49

update gunzip module

a096a96

re-use python container

02941e9

Properly handling splitted vcf files

543586d

add nf-core module cat/cat to concatenate fastas for optional --fasta…

e7d88d2

…_output flag

Optimize runtime, make sure test.config runs through

8e1a572

passing peptides and protein tests

ae2ec4a

fixes for mouse tests passing. Switching from mhc_class to and since …

b4a8a9e

…mouse has also two classes. Needs to be adjusted in nf-core test data

Robust empty variant handling

76ed93f

full test passing

6d87b06

clean up params

5781a91

jonasscheid merged commit 69080c4 into nf-core:mhc-binding-subworkflow Feb 3, 2025
2 of 18 checks passed

jonasscheid deleted the handle-variants branch February 3, 2025 07:56

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Refactor variant prediction #268

Refactor variant prediction #268

jonasscheid commented Feb 3, 2025 •

edited

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nf-core-bot commented Feb 3, 2025

github-actions bot commented Feb 3, 2025 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Refactor variant prediction #268

Refactor variant prediction #268

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jonasscheid commented Feb 3, 2025 • edited Loading

PR checklist

nf-core-bot commented Feb 3, 2025

github-actions bot commented Feb 3, 2025 • edited Loading

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jonasscheid commented Feb 3, 2025 •

edited

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github-actions bot commented Feb 3, 2025 •

edited

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`nf-core pipelines lint` overall result: Failed ❌