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Split STAR modules to fix issue with nf-core download #835

Merged
merged 1 commit into from
May 27, 2022
Merged

Split STAR modules to fix issue with nf-core download #835

merged 1 commit into from
May 27, 2022

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drpatelh
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Closes #834

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github-actions bot commented May 27, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 17577df

+| ✅ 144 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.8.1'
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-05-27 11:58:44

drpatelh
drpatelh commented May 27, 2022
View reviewed changes
conf/modules.config
@@ -58,7 +58,7 @@ process {
ext.args2 = '--no-same-owner'
}

withName: 'UNTAR_.*|STAR_GENOMEGENERATE|HISAT2_BUILD' {
withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
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@mahesh-panchal if you are around can you double-check this logic looks good. I have tested and it seems to be working but wanted a sanity check.

drpatelh
drpatelh commented May 27, 2022
View reviewed changes
conf/modules.config
@@ -495,7 +495,7 @@ if (!params.skip_alignment) {

if (!params.skip_alignment && params.aligner == 'star_salmon') {
process {
withName: '.*:ALIGN_STAR:STAR_ALIGN' {
withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
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Same here @mahesh-panchal

@drpatelh drpatelh mentioned this pull request May 27, 2022
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JoseEspinosa
JoseEspinosa approved these changes May 27, 2022
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LGTM! Well done 🚀

subworkflows/local/align_star.nf
@@ -22,24 +23,53 @@ workflow ALIGN_STAR {
//
// Map reads with STAR
//
STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center, is_aws_igenome )
ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first())
ch_orig_bam = Channel.empty()
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Out of curiosity, what orig stands for, I guess ig=ignenomes, o=output?, r ??

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orig = original 🤣 It's because STAR can generate loads of different types of BAM files.

@drpatelh drpatelh merged commit f9d3b20 into nf-core:dev May 27, 2022
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@mahesh-panchal mahesh-panchal Awaiting requested review from mahesh-panchal

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2 participants
@drpatelh @JoseEspinosa