Main merge by robert-a-forsyth · Pull Request #153 · IntGenomicsLab/lrsomatic

robert-a-forsyth · 2026-04-01T14:55:49Z

PR checklist

ASCAT GC and RT LogR correct added to hg38, GC correct to T2T.

ASCAT pdf plots, minor channel fix

Deepvariant

Added a link for more information on running the pipeline.

Modkit

github-actions · 2026-04-01T14:56:08Z

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 · 2026-04-01T14:58:15Z

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

Posted for pipeline commit 362eb65

+| ✅ 210 tests passed       |+
#| ❔  21 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  34 tests had warnings |!

Details

❗ Test warnings:

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 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 meta.yml: #Add a description of the module and list keywords
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
schema_description - No description provided in schema for parameter: autocorrelation
schema_description - No description provided in schema for parameter: vep_custom
schema_description - No description provided in schema for parameter: vep_custom_tbi
schema_description - No description provided in schema for parameter: severus_minsupport
schema_description - No description provided in schema for parameter: wakhan_chroms
local_component_structure - prepare_reference_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - deepsomatic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - phasing_haplotyping.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 - small_variant_consensus.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.germline_var_combine= all
nextflow_config - Config default value correct: params.somatic_var_combine= all
nextflow_config - Config default value correct: params.prioritize_caller_germline= deepvariant
nextflow_config - Config default value correct: params.prioritize_caller_somatic= deepsomatic
nextflow_config - Config default value correct: params.igenomes_ignore= false
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.vep_cache= s3://annotation-cache/vep_cache/
nextflow_config - Config default value correct: params.vep_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_cache_version= 113
nextflow_config - Config default value correct: params.download_vep_cache= false
nextflow_config - Config default value correct: params.severus_minsupport= 3
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.ascat_pdf_plots= false
nextflow_config - Config default value correct: params.skip_qc= false
nextflow_config - Config default value correct: params.skip_cramino= false
nextflow_config - Config default value correct: params.skip_mosdepth= false
nextflow_config - Config default value correct: params.skip_bamstats= false
nextflow_config - Config default value correct: params.skip_wakhan= false
nextflow_config - Config default value correct: params.skip_fiber= false
nextflow_config - Config default value correct: params.skip_ascat= false
nextflow_config - Config default value correct: params.skip_m6a= false
nextflow_config - Config default value correct: params.skip_vep= false
nextflow_config - Config default value correct: params.skip_normalfiber= false
nextflow_config - Config default value correct: params.skip_nanoplot= false
nextflow_config - Config default value correct: params.skip_whatshapstats= false
nextflow_config - Config default value correct: params.skip_modcall= false
nextflow_config - Config default value correct: params.use_gpu= false
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.version= false
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.plaintext_email= false
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.monochrome_logs= false
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.help= false
nextflow_config - Config default value correct: params.help_full= false
nextflow_config - Config default value correct: params.show_hidden= false
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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: claude-code-review.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: claude.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: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-04-01 14:57:54

robert-a-forsyth and others added 30 commits November 28, 2025 16:13

snap, version update

eb51d56

prettier

b5938f2

view

5b24d20

view

19b15b4

view

77ae92f

channel fix

ada3e8f

update ascat for pdf plotting

742f0ee

change var

feeee90

prettier and linting

0e9e256

views

c2c0c15

added gc and rt loci files in igenomes

623a21c

changed ascat params to include GC and RT file

b831533

linting

741e907

ASCAT GC and RT in documentation

3479917

prettier

2877f1d

quick fix

06ff17d

minor formatting

b5bbce7

remove stupid s

661f10a

correct ref path ascat GC file T2T

c07cf59

changed GC file link T2T to correct one 2.0

2c9e2e6

fix GC file ASCAT 3.0

b567356

Fix case of ascat_pdf_plots value to 'FALSE'

af58b03

Merge pull request #116 from AmberVerhasselt/dev

9eda20b

ASCAT GC and RT LogR correct added to hg38, GC correct to T2T.

Merge pull request #117 from IntGenomicsLab/hotfix

01ba648

ASCAT pdf plots, minor channel fix

Template update for nf-core/tools version 3.5.1

dcc9e4a

template merge

e637341

change versioning output to topic for all local modules

e003997

pre-commit

d777e58

mass updates of nf-core modules and subworkflows

cf01c78

minor changelog update

b01cd5e

robert-a-forsyth and others added 27 commits March 26, 2026 17:34

merge

9b28649

remove old output

9e2d555

merge

fa961d8

small changes

6f5a1b1

output fix

c8347db

Merge branch 'wakhan' into modkit

ec119b3

versioning

7e0978d

revert longphase output versions

eb86f4a

adressing comments

f094a0b

updates to documentation/process labels

4834e8c

prettier

5cfadfb

merge

f4c6a66

Merge branch 'deepvariant' into modkit

40cb855

merge

7c419ca

fix merge conflict

486156f

documentation, small fixes to config

deefcf9

Merge pull request #149 from IntGenomicsLab/deepvariant

d2cc09b

Deepvariant

Merge branch 'deepvariant' into modkit

063ba8c

Update README with additional pipeline running information

c281a73

Added a link for more information on running the pipeline.

update snap/ edit config

a2bc320

add code documentation bit

1196192

nextflow strict syntax changes

9d5caed

update patch for longphase/phase

33cd33b

linting a automatically generated file for some reason

a657d14

Merge pull request #152 from IntGenomicsLab/modkit

9081e3f

Modkit

merge

7be7f7d

fix image

362eb65

robert-a-forsyth closed this Apr 1, 2026

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Main merge#153

Main merge#153
robert-a-forsyth wants to merge 237 commits into
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robert-a-forsyth commented Apr 1, 2026

Uh oh!

github-actions Bot commented Apr 1, 2026

Uh oh!

github-actions Bot commented Apr 1, 2026

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

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robert-a-forsyth commented Apr 1, 2026

PR checklist

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github-actions Bot commented Apr 1, 2026

This PR is against the main branch ❌

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github-actions Bot commented Apr 1, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

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This PR is against the `main` branch ❌

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