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Fix #961 #963

Merged
merged 2 commits into from
Mar 17, 2023
Merged

Fix #961 #963

merged 2 commits into from
Mar 17, 2023

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drpatelh
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Closes #961

maxulysse
maxulysse approved these changes Mar 17, 2023
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I feel like the NfcoreTemplate.groovy lib is getting more and more specific to rnaseq and less TEMPLATy, should we move things out? and keep this one file only for TEMPLATE stuff?

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github-actions bot commented Mar 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6c63436

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.11.0'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ 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 2.7.2
  • Run at 2023-03-17 13:25:24

@drpatelh drpatelh merged commit eba7275 into nf-core:dev Mar 17, 2023
calizilla
calizilla reviewed Apr 20, 2023
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lib/NfcoreTemplate.groovy
def samp_aln = ''
for (samp in fail_percent_mapped) {
samp_aln += " ${samp.value}%: ${samp.key}\n"
if (fail_mapped_count > 0 || fail_trimmed_count > 0 || fail_strand_count > 0) {
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Samples that fail strandedness check are not skipped, they are still processed but a warning is printed in the multiqc report. For example a run with all 6 samples with the wrong strandedness specified in the sampelsheet, the below output is printed to terminal:

-[nf-core/rnaseq] Pipeline completed successfully with skipped sampl(es)- -[nf-core/rnaseq] Please check MultiQC report: 6/6 samples failed strandedness check.-

Can this be changed to only report 'skipped samp(les)' for samples that fail map or trim count and not strandedness. The message that samples failed strandedness check is sufficient.

A more helpful long-term solution would be to run a QC and strand check BEFORE the whole rnaseq run with alignment and counting is performed. This is more consistent with what researchers want in real life.

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@maxulysse maxulysse maxulysse approved these changes

@calizilla calizilla calizilla left review comments

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3 participants
@drpatelh @maxulysse @calizilla