Template update by ljwharbers · Pull Request #80 · IntGenomicsLab/lrsomatic

ljwharbers · 2025-08-19T13:46:46Z

Template update from 3.1.1 to 3.3.2

PR checklist

Copilot

Pull Request Overview

This PR updates the nf-core template from version 3.1.1 to 3.3.2, bringing the pipeline up to date with the latest nf-core framework standards and best practices.

Key changes include:

Migration from GitHub Actions CI workflow to nf-test testing framework
Updated dependencies including nf-schema plugin from 2.1.1 to 2.4.2 and multiqc from 1.25.1 to 1.29
Enhanced configuration for GPU support and improved error handling

Reviewed Changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
`.github/workflows/nf-test.yml`	New comprehensive nf-test workflow replacing the old CI approach
`tests/`	New testing infrastructure with nf-test configuration and test files
`nextflow.config`	Updated plugin versions, GPU support, and improved configuration loading
`modules/nf-core/multiqc/`	Updated MultiQC module to version 1.29 with enhanced metadata
`.github/workflows/`	Updated various workflow files with newer action versions and Python 3.13
`.nf-core.yml`	Template configuration updated to reflect new version and structure

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github-actions · 2025-08-19T13:54:05Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 624b83e

+| ✅ 174 tests passed       |+
#| ❔  25 tests were ignored |#
!| ❗ 157 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: List required Conda package(s).
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: List additional required output channels/values here
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: List required Conda package(s).
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: List additional required output channels/values here
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: List required Conda package(s).
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: List additional required output channels/values here
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: List required Conda package(s).
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: List additional required output channels/values here
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: List required Conda package(s).
pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in main.nf: List additional required output channels/values here
pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
local_component_structure - tumor_only_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_reference_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - tumor_normal_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-lr_somatic_logo_light.png
files_exist - File is ignored: docs/images/nf-core-lr_somatic_logo_light.png
files_exist - File is ignored: docs/images/nf-core-lr_somatic_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: validation.help.beforeText
nextflow_config - Config variable ignored: validation.help.afterText
nextflow_config - Config variable ignored: validation.summary.beforeText
nextflow_config - Config variable ignored: validation.summary.afterText
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-lr_somatic_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-lr_somatic_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-lr_somatic_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/lr_somatic/lr_somatic/.github/workflows/awstest.yml
schema_params - schema_params

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.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/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.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-lr_somatic_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/WorkflowLr_somatic.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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.command
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0.0dev
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.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.save_secondary_alignment= true
nextflow_config - Config default value correct: params.ascat_penalty= 150
nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
nextflow_config - Config default value correct: params.ascat_min_counts= 10
nextflow_config - Config default value correct: params.ascat_min_map_qual= 10
nextflow_config - Config default value correct: params.ascat_longread_bins= 2000
nextflow_config - Config default value correct: params.ascat_allelecounter_flags= -f 0
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/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml 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/sendmail_template.txt matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: nf-test.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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-09-01 14:04:30

…to template_update merge

ljwharbers · 2025-08-22T09:42:14Z

After merging latest dev include channel version of vcfsplit

…r_somatic into template_update

ljwharbers added 3 commits August 19, 2025 14:40

Template update for nf-core/tools version 3.3.2

d07894e

Template update for nf-core/tools version 3.3.2

3261a07

template merge

1fdc17a

Copilot AI review requested due to automatic review settings August 19, 2025 13:46

Copilot AI reviewed Aug 19, 2025

View reviewed changes

ljwharbers added 12 commits August 19, 2025 16:12

linting

5efbed0

fix json linting

6c097c5

restructured modules.config minimap2

10effa0

Merge branch 'dev' of https://github.com/IntGenomicsLab/lr_somatic in…

db671e1

…to template_update merge

bulk modules updates

526c33a

adjusted subworkflow for updated samtools_faidx

db3871f

added versions to all tools and emit version in lr_somatic.nf

33f2cfd

formatting and linting

3132011

prettier linting

833fb36

linting

884fbbe

added versioning of clairsto

9c53285

fix ro-crate linting

ec95289

robert-a-forsyth approved these changes Aug 20, 2025

View reviewed changes

ljwharbers added 2 commits August 20, 2025 17:21

baby change

f80f98d

move clairs to subworkflow

45b703f

ljwharbers added 8 commits August 22, 2025 15:05

revert change and disable linting of schema params

b0e4c65

skip wakhan in test profile

4d66175

dev merge

a8bfb57

linting

06b0606

remove tests

16e3b2a

remove tests

2887102

fix docker url

9f6c4db

fix docker url

9222ed5

ljwharbers and others added 20 commits August 28, 2025 13:09

clair3 biocontainers and version update

486e9b1

fix clair3 model

8467073

dev merge

9e1b134

prettier

2a5c61e

merge with clairs_move

9294b2a

clair fixes

4c65705

dev merge

fae10e2

fix preprare_references structure

c7b152a

fix channel

51c83bc

fix model name

e8842ca

fix channels

1e50377

fix naming

402cd4b

channel structure fixes

868928b

remove view

cff8b03

added clairsmodelmap

6c40391

Merge branch 'clair3_model_fix' into template_update

a00ac69

Merge branch 'template_update' of https://github.com/IntGenomicsLab/l…

ea3e40a

…r_somatic into template_update

add brackets

4fbbaa9

fix merge artifacts

6bde8da

linting

624b83e

robert-a-forsyth merged commit 4707024 into dev Sep 1, 2025
5 of 6 checks passed

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Template update#80

Template update#80
robert-a-forsyth merged 45 commits into
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ljwharbers commented Aug 19, 2025

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github-actions Bot commented Aug 19, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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ljwharbers commented Aug 22, 2025

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ljwharbers commented Aug 19, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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ljwharbers commented Aug 22, 2025

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github-actions Bot commented Aug 19, 2025 •

edited

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️