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Fastp sc #331

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mapo9
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@mapo9 mapo9 commented May 7, 2024

This pr adds the fastp module to the raw single cell based subworkflow.

@mapo9 mapo9 requested a review from ggabernet May 7, 2024 12:25
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github-actions bot commented May 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 09d135a

+| ✅ 205 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-08 13:14:53

@ggabernet ggabernet changed the base branch from dev to master May 28, 2024 23:54
@ggabernet ggabernet changed the base branch from master to dev May 28, 2024 23:54
@ggabernet ggabernet changed the base branch from dev to master November 26, 2024 02:12
@ggabernet ggabernet changed the base branch from master to dev November 26, 2024 02:12
ggabernet
ggabernet reviewed Nov 26, 2024
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modules/local/rename_fastq_cellranger.nf
tuple val(meta_2), path(orig_r1), path(orig_r2)

output:
tuple val(meta), path('*R1_001.fastq.gz'), path('*R2_001.fastq.gz') , emit: reads
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The files won't necessarily end with R1_001.fastq.gz unless we force them to be named this way. Would it be a possibility to rename at this step the fastq files so that they have the name that cellranger expects? We have to be careful with different files from the same sample that correspond to different lanes though

modules/local/rename_fastq_cellranger.nf

script:
"""
mv ${R1} fastp_${orig_r1}
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Why adding fastp at the beginning of the filenames?

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@mapo9 @ggabernet