Important! Template update for nf-core/tools v2.9 #95

nf-core-bot · 2023-06-30T16:58:52Z

Version 2.9 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.9 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/developers/sync.

For more information about this release of nf-core/tools, please see the v2.9 release page.

github-actions · 2023-09-14T10:21:35Z

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

Posted for pipeline commit a23a895

+| ✅ 156 tests passed       |+
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
system_exit - System.exit in WorkflowRnavar.groovy: System.exit(1) [line 24]
system_exit - System.exit in WorkflowRnavar.groovy: System.exit(1) [line 29]
system_exit - System.exit in WorkflowRnavar.groovy: System.exit(1) [line 34]
system_exit - System.exit in WorkflowRnavar.groovy: System.exit(1) [line 39]

✅ 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: CODE_OF_CONDUCT.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/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: assets/nf-core-rnavar_logo_light.png
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/images/nf-core-rnavar_logo_light.png
files_exist - File found: docs/images/nf-core-rnavar_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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowRnavar.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-rnavar_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: .travis.yml
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: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 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 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
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE 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 - assets/nf-core-rnavar_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnavar_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnavar_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.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: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (171 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.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' 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'

Run details

nf-core/tools version 2.9
Run at 2023-09-21 07:01:07

assets/schema_input.json

bin/check_samplesheet.py

CarsonJM · 2023-09-20T15:08:27Z

modules/local/gtf2bed/main.nf

Add stub to this local module?

CarsonJM · 2023-09-20T15:18:33Z

subworkflows/local/bam_markduplicates/main.nf

+    emit:
+    bam     = ch_bam_index
+    reports = ch_reports
+


Suggested change

CarsonJM · 2023-09-20T15:18:57Z

subworkflows/local/bam_sort_samtools/main.nf

    bam      = SAMTOOLS_SORT.out.bam           // channel: [ val(meta), [ bam ] ]
    bai      = SAMTOOLS_INDEX.out.bai          // channel: [ val(meta), [ bai ] ]
    csi      = SAMTOOLS_INDEX.out.csi          // channel: [ val(meta), [ csi ] ]



Suggested change

CarsonJM · 2023-09-20T15:19:10Z

subworkflows/local/cram_qc_mosdepth_samtools/main.nf

+
+    emit:
+    reports
+


Suggested change

maxulysse · 2023-09-20T16:04:58Z

Thanks a lot @CarsonJM.
I fixed your comments apart from the stub and the code polishing which I'll do in separate PRs.

SPPearce

Looks good to me, great start Maxime.

nextflow_schema.json

nf-core-bot and others added 8 commits August 30, 2022 13:37

Template update for nf-core/tools version 2.5

3149533

Template update for nf-core/tools version 2.5.1

c0049b9

Template update for nf-core/tools version 2.6

dca413e

Template update for nf-core/tools version 2.7.1

681ca7e

Template update for nf-core/tools version 2.7.2

e5294c1

merge template and update modules

c85b8a0

Template update for nf-core/tools version 2.8

feac580

Template update for nf-core/tools version 2.9

259c1c4

nf-core-bot mentioned this pull request Jun 30, 2023

Important! Template update for nf-core/tools v2.8 #91

Closed

Merge branch 'dev' into nf-core-template-merge-2.9

3248729

maxulysse added 19 commits September 14, 2023 12:23

typo

dd90d55

update all modules

6331c14

prettier

4976312

fix lint

0a001cd

fix path to file

a2856bd

add file

c205c24

typo + code polish

f7ae880

fix path to modules

64a3dcd

update all modules + fix path to subworkflows

519f412

improve prepare_genome subworkflow

b3427df

use samplesheet from nf-validation

3663ecb

one more step

4e44c19

markduplicates

65b3343

splitncigar

fc9cbc2

baserecalibrator

d8e927f

recalibrate

1ce3369

haplotypecaller

6669292

HAPLOTYPECALLERGVCF

40128c7

multiqc

0bf28e0

maxulysse added 6 commits September 20, 2023 14:15

update tests

90600fe

remove annotation tests

1cd7988

fix test csi

05cb821

fix tests

e32e8e8

uncomment

8858819

fix csi tests

80503cc

maxulysse approved these changes Sep 20, 2023

View reviewed changes

CarsonJM approved these changes Sep 20, 2023

View reviewed changes

fix comments from review

cfeeeb4

SPPearce approved these changes Sep 21, 2023

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

update schema

a23a895

maxulysse merged commit 3664dfa into dev Sep 21, 2023

maxulysse deleted the nf-core-template-merge-2.9 branch September 21, 2023 07:50

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Important! Template update for nf-core/tools v2.9 #95

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❗ Test warnings:

✅ Tests passed:

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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github-actions bot commented Sep 14, 2023 •

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