[DO NOT MERGE] - Core pipeline review by maxulysse · Pull Request #65 · nf-core/rnadnavar

maxulysse · 2025-12-08T16:16:31Z

I created this against the latest commit in the template branch that I put in a separate branch (template_3.5.1).

PR checklist

Important! Template update for nf-core/tools v2.12 As Maxime says, we will fix the linting when we update the modules and subworkflows.

Important! Template update for nf-core/tools v2.13.1 Linting was also updated

Fixing channel of gzi in MERGE_CRAM

…t (memory consuming)

…to cleanup_and_testing

Cleanup and testing

First release prep

github-actions · 2025-12-08T16:19:23Z

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

Posted for pipeline commit 26df4e3

+| ✅ 224 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0
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: 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 base.config: Check the defaults for all processes
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
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_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: assets/nf-core-rnadnavar_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-rnadnavar_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-rnadnavar_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
template_strings - template_strings
modules_config - modules_config

✅ 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: CODE_OF_CONDUCT.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/config.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: assets/nf-core-rnadnavar_logo_light.png
files_exist - File found: docs/images/nf-core-rnadnavar_logo_light.png
files_exist - File found: docs/images/nf-core-rnadnavar_logo_dark.png
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-rnadnavar_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/WorkflowRnadnavar.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.name
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: manifest.homePage
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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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.split_fastq= 50000000
nextflow_config - Config default value correct: params.step= mapping
nextflow_config - Config default value correct: params.rna= true
nextflow_config - Config default value correct: params.dna= true
nextflow_config - Config default value correct: params.genome= GRCh38
nextflow_config - Config default value correct: params.star_max_memory_bamsort= 0
nextflow_config - Config default value correct: params.star_bins_bamsort= 50
nextflow_config - Config default value correct: params.star_max_collapsed_junc= 1000000
nextflow_config - Config default value correct: params.read_length= 76.0
nextflow_config - Config default value correct: params.nucleotides_per_second= 200000.0
nextflow_config - Config default value correct: params.igenomes_ignore= false
nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.trim_nextseq= 0
nextflow_config - Config default value correct: params.aligner= bwa-mem
nextflow_config - Config default value correct: params.defaultvariantcallers= sage,strelka,mutect2
nextflow_config - Config default value correct: params.gatk_interval_scatter_count= 25
nextflow_config - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
nextflow_config - Config default value correct: params.vep_custom_args= --no_progress --offline --shift_hgvs 1 --check_existing --tsl --domains --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --biotype --force_overwrite --sift p --polyphen p --variant_class --regulatory --allele_number --af_gnomad --af_gnomadg --gene_phenotype --hgvs --hgvsg --max_af
nextflow_config - Config default value correct: params.vep_out_format= vcf
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/rnadnavar/
nextflow_config - Config default value correct: params.modules_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/
nextflow_config - Config default value correct: params.seq_platform= ILLUMINA
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
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/test_full.nf.test' contains outdir parameter
nf_test_content - 'tests/test_full.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_full.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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md 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
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
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
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
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: release-announcements.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.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 a matching 'report_comment'.
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 subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - BWAMEM1_MEM found in conf/base.config and Nextflow scripts.
base_config - MUTECT2_PAIRED found in conf/base.config and Nextflow scripts.
base_config - ENSEMBLVEP_VEP found in conf/base.config and Nextflow scripts.
base_config - FASTQC found in conf/base.config and Nextflow scripts.
base_config - MULTIQC found in conf/base.config and Nextflow scripts.
base_config - GATK4_APPLYBQSR found in conf/base.config and Nextflow scripts.
base_config - GATK4_GATHERBQSRREPORTS found in conf/base.config and Nextflow scripts.
base_config - GATK4_MARKDUPLICATES found in conf/base.config and Nextflow scripts.
base_config - STRELKA found in conf/base.config and Nextflow scripts.
base_config - PICARD_FILTERSAMREADS found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_EXTRACT_READ_IDS found in conf/base.config and Nextflow scripts.
base_config - GATK4_CREATESEQUENCEDICTIONARY found in conf/base.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 2025-12-08 16:19:04

FriederikeHanssen · 2026-01-20T15:21:34Z

@maxulysse pinging you as a reminder ;) Do we need to find a second reviewer still?

RaqManzano and others added 30 commits February 14, 2024 14:20

Merging nre template

1e15285

fix merge conflicts

be31e66

fix lint

97be423

Merge pull request #25 from nf-core/nf-core-template-merge-2.12

1d0d9c3

Important! Template update for nf-core/tools v2.12 As Maxime says, we will fix the linting when we update the modules and subworkflows.

Changed config

4bb4e93

Updating modules and subworkflows

6afa2dc

Fix tools

3d72c04

Fixed samplesheet check and README. Removed SAGE from full_test for now.

895581f

Renaming step

de80e5c

fixing merge conflicts

1451883

getting back some files from the emrge

8b919b3

small fixes to configs

f22561b

fix merge

22bd452

fix merge

f0cc684

Implemented utils subworkflow and removed groovy scripts

2d37d52

module update

30812fb

solved logo lint

0a994a5

prettier

adcba31

prettier + linting

7c5d57b

Merge pull request #27 from nf-core/nf-core-template-merge-2.13.1

4e0bf2b

Important! Template update for nf-core/tools v2.13.1 Linting was also updated

config minor changes and clean-up

03b81f2

module and subworkflow updates

89567a2

changing bin permissions to executable

aebbdb4

Updated ensembl and tabix/bgzip modules

162def6

Updated sage module

44fd63f

Renamed second_run to realignment

d2a0722

Modified rna_filtering to accept different scenarios

09ed5dd

Added gzi index

1ef152e

Renamed second_run to realignment

681a6ac

Updated vep_cache and multiqc chunk

cc8abd3

RaqManzano and others added 27 commits November 11, 2025 10:21

Merge pull request #58 from nf-core/patch_cram_merge_index_samtools

d277f22

Fixing channel of gzi in MERGE_CRAM

Fixed maf pattern in schema

6e5ea6e

Fixed csv from consensus step.

f8e7132

Added condition to plotting considering total number of muts in outpu…

08837b7

…t (memory consuming)

manta config no longer used

7d48acf

improved normal_id handling in samplesheet_to_channel

4f9ee7b

removed unused lines

239573a

fix on vep init when realignment

21afe6e

test cleanup

c3a9a68

Merge remote-tracking branch 'origin/nf-core-template-merge-3.5.1' in…

95d124b

…to cleanup_and_testing

clean up

3bb96a5

clean up

f11b962

pre-commit fix

d04f977

test updates

578a699

small fix to nf-test

a757536

updated snap

932ca65

Merge pull request #60 from nf-core/cleanup_and_testing

840feac

Cleanup and testing

changing version

fe9455a

version and pipeline description in ro-crate

785bd18

Added citations

7dc6a2a

version to numeric

c0c6043

Added more details to docs

f89437c

prettier

b8a29cf

Added citation

6b197ca

removing old enable_conda param

75f6823

updated tests

a5b0be0

Merge pull request #63 from nf-core/first-release

26df4e3

First release prep

maxulysse self-assigned this Dec 8, 2025

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[DO NOT MERGE] - Core pipeline review#65

[DO NOT MERGE] - Core pipeline review#65
maxulysse wants to merge 534 commits intotemplate_3.5.1from
dev

maxulysse commented Dec 8, 2025

Uh oh!

github-actions bot commented Dec 8, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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FriederikeHanssen commented Jan 20, 2026

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maxulysse commented Dec 8, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

FriederikeHanssen commented Jan 20, 2026

Uh oh!

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github-actions bot commented Dec 8, 2025 •

edited

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