From d91a71d57ca688b88cd311e4fa7d30165946c1ba Mon Sep 17 00:00:00 2001
From: mherbett <marion.herbette@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:18:05 +0000
Subject: [PATCH] RNASeq.nf : mov cod o qualiy imin, kp adaptao rmoval
---
src/RNASeq.nf | 63 ---------------------------------------------------
1 file changed, 63 deletions(-)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index e8f6bb4..c130936 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -38,66 +38,3 @@ process adaptor_removal {
"""
}
-/* quality trimming */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process trimming {
- tag "$pair_id"
- publishDir "results/fastq/trimming/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
-
- script:
- """
- cutadapt -q 20,20 \
- -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
- ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
- """
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process trimming {
- tag "$reads.baseName"
- publishDir "results/fastq/trimming/", mode: 'copy'
-
- input:
- file reads from fastq_files
-
- output:
- file "*_trim.fastq.gz" into fastq_files_trim
-
- script:
- """
- cutadapt -q 20,20 \
- -o ${reads.baseName}_trim.fastq.gz \
- ${reads} > ${reads.baseName}_report.txt
- """
-}
--
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