Documentation by robert-a-forsyth · Pull Request #106 · IntGenomicsLab/lrsomatic

robert-a-forsyth · 2025-11-27T11:52:49Z

PR checklist

github-actions · 2025-11-27T11:54:50Z

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

Posted for pipeline commit 2da4897

+| ✅ 177 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗ 148 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 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 lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
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: 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 main.nf: Remove this line if you don't need a FASTA file
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 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 nextflow.config: Specify any additional parameters here
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: 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: 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
local_component_structure - tumor_only_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_annotation.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-lrsomatic_logo_light.png
files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_light.png
files_exist - File is ignored: docs/images/nf-core-lrsomatic_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
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-lrsomatic_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/lrsomatic/lrsomatic/.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-lrsomatic_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/WorkflowLrsomatic.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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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/
nextflow_config - Config default value correct: params.normal_fiber= true
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: 25.04.0, Config: 25.04.0
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
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_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.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.
modules_config - ENSEMBLVEP_DOWNLOAD 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2025-11-28 10:41:06

Copilot

Pull request overview

This PR primarily updates pipeline documentation and dependencies, removes debug code, and makes several configuration and module updates.

Key Changes

Updated documentation in docs/usage.md and docs/output.md with comprehensive parameter descriptions and output structure
Removed debug .view() calls from workflows/lrsomatic.nf
Updated module versions (MultiQC 1.30→1.32, VEP, LongPhase, etc.)
Added help message support via nf-schema plugin
Updated Nextflow version requirement (24.10.5→25.04.0)

Reviewed changes

Copilot reviewed 49 out of 50 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
workflows/lrsomatic.nf	Removed debug `.view()` statements for cleaner code
docs/usage.md	Added comprehensive parameter documentation and usage examples
docs/output.md	Complete rewrite with detailed output structure documentation
modules/local/clairs/main.nf	Added indel calling flag and haplotagging skip option
subworkflows/nf-core/utils_nfschema_plugin/main.nf	Added help message functionality
subworkflows/local/tumor_normal_happhase.nf	Added `size: 2` to `groupTuple()` for paired samples
modules.json	Updated module versions and git SHAs
nextflow.config	Updated minimum Nextflow version requirement
Multiple test files	Updated snapshots and test configurations

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

You can also share your feedback on Copilot code review for a chance to win a $100 gift card. Take the survey.

Copilot · 2025-11-27T11:55:46Z

 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML()))


Incorrect case for channel factory method: channel.of() should be Channel.of() (capital C). The lowercase version is deprecated and may cause issues.

Copilot · 2025-11-27T11:55:46Z

    main:

-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()


Inconsistent casing for channel factory method: should be Channel.empty() (capital C) instead of channel.empty() to match Nextflow conventions and other usages in the codebase.

Copilot · 2025-11-27T11:55:46Z

    //

-    Channel
+    channel


Inconsistent casing for channel factory method: should be Channel.fromList() (capital C) instead of channel.fromList() to match Nextflow conventions and other usages in the codebase.

Copilot · 2025-11-27T11:55:47Z

            return[new_meta, [[type: meta.type], hapbam], [[type: meta.type], hapbai]]
        }
-        .groupTuple()
+        .groupTuple(size: 2)


The size: 2 parameter in groupTuple() assumes exactly 2 samples (tumor and normal). This could cause the pipeline to hang or fail if a sample doesn't have both tumor and normal data. Consider adding error handling or documenting this requirement clearly.

Copilot · 2025-11-27T11:55:47Z

        --normal_bam_fn $normal_bam \\
        --ref_fn $reference \\
        --threads $task.cpus \\
+        --enable_indel_calling \\


The new flag --haplotagged_tumor_bam_provided_so_skip_intermediate_phasing_and_haplotagging is added without documentation. Consider adding a comment explaining why this flag is needed and what assumptions it makes about the input data.

Suggested change

--enable_indel_calling \\

--enable_indel_calling \\

# The following flag indicates that the input tumor BAM file is already haplotagged.

# This allows the pipeline to skip intermediate phasing and haplotagging steps.

# Assumes that the input BAM is properly haplotagged and suitable for downstream analysis.

Co-authored-by: ljwharbers <40829819+ljwharbers@users.noreply.github.com>

Add bibliography of tools used in pipeline

ljwharbers

After adding wakhan and multiqc in output description, ready to go.

robert-a-forsyth added 7 commits November 20, 2025 16:01

Fix input

f26893d

revert

faf07bb

improve file structures

29f81d0

update file descriptions

5a3b72b

fix file descriptions

6ee0718

updates to file descriptions

5859b29

extra touches

e781f03

Copilot AI review requested due to automatic review settings November 27, 2025 11:52

Copilot started reviewing on behalf of robert-a-forsyth November 27, 2025 11:53 View session

Copilot finished reviewing on behalf of robert-a-forsyth November 27, 2025 11:54

Copilot AI reviewed Nov 27, 2025

View reviewed changes

robert-a-forsyth and others added 8 commits November 27, 2025 12:56

add samtools info

6955466

Checkpoint from VS Code for coding agent session

e108960

Add bibliography of tools used in pipeline to CITATIONS.md

c716e65

Co-authored-by: ljwharbers <40829819+ljwharbers@users.noreply.github.com>

Merge pull request #107 from IntGenomicsLab/copilot/uncomfortable-mink

144f3ee

Add bibliography of tools used in pipeline

fix citations

0dcd704

remove todo

5a991a6

removed TODOs and added citations

14f6b90

Contributions

d11787e

ljwharbers approved these changes Nov 27, 2025

View reviewed changes

robert-a-forsyth added 5 commits November 27, 2025 17:17

add wakhan

22c616b

multi-qc + wakhan

5e73c3c

Merge branch 'dev' into documentation

6995233

update lint

0fb11da

prettier

2da4897

robert-a-forsyth merged commit bff2248 into dev Nov 28, 2025
7 checks passed

robert-a-forsyth deleted the documentation branch November 28, 2025 12:11

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Documentation#106

Documentation#106
robert-a-forsyth merged 20 commits into
devfrom
documentation

robert-a-forsyth commented Nov 27, 2025

Uh oh!

github-actions Bot commented Nov 27, 2025 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Copilot AI Nov 27, 2025

Uh oh!

Copilot AI Nov 27, 2025

Uh oh!

Copilot AI Nov 27, 2025

Uh oh!

Copilot AI Nov 27, 2025

Uh oh!

Copilot AI Nov 27, 2025

Uh oh!

ljwharbers left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

                   //
-                  Channel
+                  channel

-        --enable_indel_calling \\
+        --enable_indel_calling \\
+        # The following flag indicates that the input tumor BAM file is already haplotagged.
+        # This allows the pipeline to skip intermediate phasing and haplotagging steps.
+        # Assumes that the input BAM is properly haplotagged and suitable for downstream analysis.

Conversation

robert-a-forsyth commented Nov 27, 2025

PR checklist

Uh oh!

github-actions Bot commented Nov 27, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Key Changes

Reviewed changes

Uh oh!

Uh oh!

Copilot AI Nov 27, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 27, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 27, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 27, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 27, 2025

Choose a reason for hiding this comment

Uh oh!

ljwharbers left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

github-actions Bot commented Nov 27, 2025 •

edited

Loading

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