Template by robert-a-forsyth · Pull Request #103 · IntGenomicsLab/lrsomatic

robert-a-forsyth · 2025-11-19T13:22:47Z

PR checklist

Copilot

Pull Request Overview

This PR appears to be an accidental template reset that has reverted the pipeline to its initial nf-core template state, effectively removing all functional pipeline code. The title "Template" and the removal of nearly all working code suggests this is not an intentional update but rather a mistaken commit or merge.

The entire core workflow logic has been stripped from workflows/lrsomatic.nf, removing all analysis steps
Input schema has been changed from BAM files to FASTQ files, incompatible with the pipeline's purpose
All pipeline-specific parameters have been removed from configuration files
Nearly all nf-core modules except MultiQC have been removed from the pipeline

Reviewed Changes

Copilot reviewed 44 out of 45 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
workflows/lrsomatic.nf	Removed all core pipeline functionality (alignment, variant calling, phasing, QC), leaving only MultiQC
assets/schema_input.json	Changed input schema from BAM files (bam_tumor, bam_normal, platform, sex, fiber) to FASTQ files (fastq_1, fastq_2)
nextflow.config	Removed all pipeline-specific parameters (VEP, minimap2, ASCAT, skip options, etc.)
nextflow_schema.json	Removed parameter definitions for minimap2_options, ascat_parameters, and skip_options sections
modules.json	Removed nearly all nf-core modules (ASCAT, ENSEMBLVEP, LONGPHASE, MINIMAP2, MOSDEPTH, SAMTOOLS, SEVERUS, etc.)
conf/test.config	Changed test data from lrsomatic-specific data to generic viralrecon template data
README.md	Replaced detailed pipeline description with generic template placeholder and changed samplesheet format
subworkflows/local/tumor_normal_happhase.nf	Added debug `.view()` statement and `groupTuple(size: 2)` parameter; changed ClairS output reference
modules/local/clairs/main.nf	Added separate outputs for indel and SNV VCFs with new flags
subworkflows/local/prepare_reference_files.nf	Added fallback to meta.clair3_model when basecall_model_meta is null
Various test and GitHub workflow files	Updated dependencies, versions, and test configurations

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Copilot · 2025-11-19T13:32:17Z

-    skip_ascat         = true
+    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references


Missing space before inline comment. There should be a space between the path string and the comment // Genome references.

Suggested change

input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references

input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' // Genome references

Copilot · 2025-11-19T13:32:18Z

+**IntGenomicsLab/lrsomatic** is a bioinformatics pipeline that ...

-This **end-to-end pipeline** handles the entire workflow — **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.
-
-It can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.
-
-Developed using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.
-
-## Pipeline summary
-
-**1) Pre-processing:**
-
-a. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))
-
-b. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))
-
-c. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))
-
-d. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))
-
-**2i) Matched mode: small variant calling:**
-
-a. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))
-
-b. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))
-
-c. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))
-
-**2ii) Tumour only mode: small variant calling:**
-
-a. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))
-
-b. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))
-
-**3) Large variant calling:**
-
-a. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))
-
-b. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))
+<!-- TODO nf-core:
+   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
+   major pipeline sections and the types of output it produces. You're giving an overview to someone new
+   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
+-->


The README description has been replaced with a generic template placeholder ("IntGenomicsLab/lrsomatic is a bioinformatics pipeline that ..."). The original comprehensive description of the pipeline's purpose, features, and capabilities has been removed, leaving users without proper documentation of what the pipeline does.

github-actions · 2025-11-20T11:07:23Z

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

Posted for pipeline commit 129acab

+| ✅ 177 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗ 155 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: Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in 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 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_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 output.md: Write this documentation describing your workflow's output
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 08:23:55

ljwharbers

ascat, minimap2, and samtools-stats diff files no longer needed or?

ljwharbers · 2025-11-20T17:37:39Z

+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
        with:
          fetch-depth: 0



I put this in manually before since otherwise sometimes the CIs crash because of no disk space.

ljwharbers · 2025-11-24T09:59:57Z

All these should be reverted as well I think @robert-a-forsyth

Copilot · 2025-11-24T10:14:29Z

@robert-a-forsyth I've opened a new pull request, #104, to work on those changes. Once the pull request is ready, I'll request review from you.

ljwharbers

Looks good to me after all tests pass

robert-a-forsyth added 5 commits November 19, 2025 11:46

Template update for nf-core/tools version 3.2.0

dc30631

Template update for nf-core/tools version 3.2.0

28ffe69

Template update for nf-core/tools version 3.2.0

09e76f5

Template update for nf-core/tools version 3.4.1

b57b036

update template

b5873ab

Copilot AI review requested due to automatic review settings November 19, 2025 13:22

Copilot started reviewing on behalf of robert-a-forsyth November 19, 2025 13:23 View session

Copilot finished reviewing on behalf of robert-a-forsyth November 19, 2025 13:26

Copilot AI reviewed Nov 19, 2025

View reviewed changes

robert-a-forsyth added 3 commits November 20, 2025 10:56

Template update for nf-core/tools version 3.5.1

8ad5e9d

template update 3.5

1780652

lint fix

c23c967

robert-a-forsyth added 3 commits November 20, 2025 13:31

update snapshot, revert test changes

1f610c4

linting fix

c64acc8

precommit

1eddb33

robert-a-forsyth assigned robert-a-forsyth and ljwharbers Nov 20, 2025

robert-a-forsyth and others added 3 commits November 20, 2025 14:27

revert readme

a0b10e1

add disk clean up back in

a5a343f

or branch is still "main" so would keep it like it was

170e72b

ljwharbers reviewed Nov 20, 2025

View reviewed changes

ljwharbers added 2 commits November 20, 2025 18:45

revert some changes

815f255

revert more

14d4b7b

ljwharbers requested changes Nov 20, 2025

View reviewed changes

Comment thread nextflow_schema.json Outdated

linting and nextflow badge

ccd84a1

ljwharbers reviewed Nov 24, 2025

View reviewed changes

Comment thread nextflow_schema.json

ljwharbers Nov 24, 2025

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All these should be reverted as well I think @robert-a-forsyth

Copilot AI mentioned this pull request Nov 24, 2025

Remove debug statement from tumor_normal_happhase workflow #104

Closed

10 tasks

Update JSON schema

b60d5f4

robert-a-forsyth added 2 commits November 25, 2025 12:35

update test snap

67b6f9a

update snap

cffc36f

ljwharbers approved these changes Nov 26, 2025

View reviewed changes

ljwharbers and others added 3 commits November 27, 2025 16:33

Merge branch 'dev' into pr/robert-a-forsyth/103

5b10063

pre-commit

e1d6fc7

snap update

129acab

robert-a-forsyth merged commit 824afdc into dev Nov 28, 2025
7 checks passed

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

	input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references
	input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' // Genome references

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robert-a-forsyth commented Nov 19, 2025

PR checklist

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github-actions Bot commented Nov 20, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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Copilot AI commented Nov 24, 2025

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github-actions Bot commented Nov 20, 2025 •

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