nf-core_modules/tests/modules/fastp/nextflow.config at 7e8ad566883449e7939062b5e2bcf53fc1e0002f - millironx/nf-core_modules - Milliron X Code: Code hosting for cattle or technology, but especially anything to do with both of them

millironx/nf-core_modules

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Adam Talbot 7e8ad56688

module FASTP: Support for interleaved FASTQ (#1891 )

* 1882 FASTP now supports interleaved FASTQ files

Changes:
 - single_end FASTP pipes the FASTQ file
 - Using args, it can be configured for interleaved in `--interleaved_in`
 - Out is automatically interleaved if input is paired end.
 - Removed md5sum checks for FASTQ files as compression seemed to cause
 differences
 - Instead, we check inside the FASTQ files for content.

Relates to #1882

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

2022-07-19 16:27:15 +01:00

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 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: '.*test_fastp_interleaved:FASTP' {
         ext.args = "--interleaved_in"
     }
 }