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

Merged
merged 36 commits into from
Sep 21, 2023
Merged

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

merged 36 commits into from
Sep 21, 2023

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nf-core-bot
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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.

@nf-core-bot nf-core-bot mentioned this pull request Jun 30, 2023
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github-actions bot commented Sep 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a23a895

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

❗ 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:

Run details

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

CarsonJM
CarsonJM approved these changes Sep 20, 2023
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assets/schema_input.json Show resolved Hide resolved
bin/check_samplesheet.py Outdated Show resolved Hide resolved
modules/local/gtf2bed/main.nf Outdated
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Add stub to this local module?

subworkflows/local/bam_markduplicates/main.nf
emit:
bam = ch_bam_index
reports = ch_reports

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Suggested change

subworkflows/local/bam_sort_samtools/main.nf
BAM_STATS_SAMTOOLS(ch_bam_bai)

reports = BAM_STATS_SAMTOOLS.out.reports.map{meta, logs -> [logs] }

ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first())

emit:
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 ] ]

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Suggested change

subworkflows/local/cram_qc_mosdepth_samtools/main.nf

emit:
reports

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Suggested change

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

SPPearce
SPPearce approved these changes Sep 21, 2023
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Looks good to me, great start Maxime.

nextflow_schema.json Outdated Show resolved Hide resolved
@maxulysse maxulysse merged commit 3664dfa into dev Sep 21, 2023
@maxulysse maxulysse deleted the nf-core-template-merge-2.9 branch September 21, 2023 07:50
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@maxulysse maxulysse maxulysse approved these changes

@CarsonJM CarsonJM CarsonJM approved these changes

@SPPearce SPPearce SPPearce approved these changes

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@nf-core-bot @maxulysse @SPPearce @CarsonJM