Hotfix

[robert-a-forsyth]

Adds ASCAT pdf printing as option and slight channel structure fix for multiple custom model downloads.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @robert-a-forsyth,

It looks like this pull-request is has been made against the IntGenomicsLab/lrsomatic main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the IntGenomicsLab/lrsomatic dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c2c0c15

+| ✅ 178 tests passed       |+
#| ❔  21 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗ 144 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• 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 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 fixed:

• rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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: 1.1.0dev
• 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.
• readme - README Zenodo placeholder was replaced with DOI.
• 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 description matches the README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2025-12-19 09:53:46

[Copilot]

Pull request overview

This is a hotfix PR that adds ASCAT PDF plotting as a configurable option and fixes channel structure issues for multiple custom model downloads. The PR also includes version bump to v1.1.0dev and updates project metadata with the official Zenodo DOI.

• Adds configurable PDF plot generation for ASCAT copy number analysis
• Fixes basecall_model handling in tumor/normal sample processing to properly use clair3_model when specified
• Updates version from v1.0.0 to v1.1.0dev with corresponding metadata changes

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
workflows/lrsomatic.nf	Adds debug view() statements (should be removed)
subworkflows/local/tumor_normal_happhase.nf	Fixes basecall_model assignment to use clair3_model when available; adds multiple debug view() statements (should be removed)
modules/nf-core/ascat/main.nf	Adds pdf_plots parameter to ASCAT runAscat calls, enabling configurable PDF output
nextflow.config	Adds ascat_pdf_plots parameter (default "False") and updates version to v1.1.0dev
conf/modules.config	Passes pdf_plots parameter to ASCAT process configuration
tests/default.nf.test.snap	Updates version reference and test timestamp
ro-crate-metadata.json	Updates version, URLs, status, and UUIDs for v1.1.0dev
README.md	Updates Zenodo DOI from placeholder to actual DOI (10.5281/zenodo.17751829)
CHANGELOG.md	Adds v1.1.0 section and marks v1.0.0 release date
.nf-core.yml	Updates template version to v1.1.0dev
assets/multiqc_config.yml	Updates report link from v1.0.0 release to dev branch

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[Copilot]

Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Suggested change

tumor_bams.view()

[Copilot]

Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

[Copilot]

Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Suggested change

downloaded_model_files.view()

[Copilot]

Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

[Copilot]

Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

[Copilot]

Debug view() statements should be removed before merging. These appear to be temporary debugging code left in the subworkflow.

Suggested change

	tumor_bams.view()
	LONGPHASE_PHASE.out.vcf.view()

[Copilot]

Debug view() statements should be removed before merging. These appear to be temporary debugging code left in the workflow and will clutter the execution logs with channel contents.

Suggested change

	wakhan_input.view()
	ch_fasta.view()

[Copilot]

The value of pdf_plots coming from args.pdf_plots is interpolated directly into the R script inside a quoted string (pdfPlot = "$pdf_plots"), so a malicious CLI parameter containing double quotes can break out of the string literal and inject arbitrary R code (for example by calling system()) in the ASCAT container. This means anyone who can control pipeline parameters can achieve code execution in the context of this process. Please constrain args.pdf_plots to a small, fixed set of safe values (e.g. a boolean) or ensure it is properly escaped/sanitized before interpolation, and apply the same hardening pattern to any other task.ext.args that are inserted into R code.