Wakhan

[ljwharbers]

PR checklist

• 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).

[Copilot]

Pull Request Overview

This PR enables the WAKHAN module in the lr_somatic pipeline, which was previously commented out. WAKHAN is a tool for copy number analysis and visualization from long-read sequencing data.

• Uncomments and fixes the WAKHAN workflow integration with proper input channel preparation
• Updates WAKHAN module to version 0.1.2 with comprehensive output definitions
• Adds configuration parameters and test settings for WAKHAN chromosome selection

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
workflows/lr_somatic.nf	Enables WAKHAN workflow and fixes input channel preparation
modules/local/wakhan/main.nf	Updates to WAKHAN v0.1.2 with proper output definitions and cleanup
nextflow.config	Adds wakhan_chroms parameter for chromosome selection
conf/modules.config	Adds WAKHAN process configuration with chromosome filtering and publish settings
conf/test.config	Adds test configuration for WAKHAN with chromosome restriction
subworkflows/local/prepare_reference_files.nf	Adds empty channel initialization for ASCAT files when not used
modules/local/vcfsplit/main.nf	Improves germline VCF processing with proper intermediate file handling

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

[Copilot]

There are trailing spaces at the end of the container URL string which should be removed.

Suggested change

	'biocontainers/wakhan:0.1.2--pyhdfd78af_0 ' }"
	'https://depot.galaxyproject.org/singularity/wakhan:0.1.2--pyhdfd78af_0':
	'biocontainers/wakhan:0.1.2--pyhdfd78af_0' }"

[Copilot]

There are trailing spaces at the end of the container URL string which should be removed.

Suggested change

	'biocontainers/wakhan:0.1.2--pyhdfd78af_0 ' }"
	'https://depot.galaxyproject.org/singularity/wakhan:0.1.2--pyhdfd78af_0':
	'biocontainers/wakhan:0.1.2--pyhdfd78af_0' }"

[Copilot]

The awk command uses $7 which escapes the dollar sign unnecessarily. In shell scripts within Nextflow, this should be $7 since the variable substitution is handled by the shell, not Nextflow template expansion.

Suggested change

	bcftools view germline_tmp.vcf.gz | awk 'BEGIN{FS=OFS="\t"} /^#/ {print} !/^#/ { \$7="PASS"; print }' | \
	bcftools view germline_tmp.vcf.gz | awk 'BEGIN{FS=OFS="\t"} /^#/ {print} !/^#/ { $7="PASS"; print }' | \

[github-actions]

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit a2cd9f4

+| ✅ 158 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗ 215 tests had warnings |!
-| ❌   2 tests failed       |-

Details

❌ Test failures:

• nextflow_config - Config default value incorrect: params.ascat_longread_bins is set as 1000 in nextflow_schema.json but is 2000 in nextflow.config.
• schema_params - Param wakhan_chroms from nextflow config not found in nextflow_schema.json

❗ 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 ro-crate-metadata.json: "description": "# IntGenomicsLab/lr_somatic\n\n\n\n\n\n\n\n\n\n\n\n## Introduction\n\nIntGenomicsLab/lr_somatic is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run IntGenomicsLab/lr_somatic \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Jonas Demeulemeester.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use IntGenomicsLab/lr_somatic for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nThis pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
• 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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 main.nf.test: Once you have added the required tests, please run the following command to build this file:
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
• pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
• pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
• pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
• pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test 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 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

❔ 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

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• 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/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: 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: 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_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/
• 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_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
• 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: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: ci.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'
• 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: 3.1.1

Run details

• nf-core/tools version 3.1.1
• Run at 2025-08-28 08:19:01