From 4d08a5979a7cebe0376332c310b792ac95d4d1cf Mon Sep 17 00:00:00 2001
From: gael <gael@ornati.biologie.ens-lyon.fr>
Date: Thu, 14 Jun 2018 17:57:08 +0200
Subject: [PATCH] RNASeq.nf: remove single-end process
---
src/RNASeq.nf | 32 --------------------------------
1 file changed, 32 deletions(-)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index a7fca65..74a7150 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -36,35 +36,3 @@ process adaptor_removal {
${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: ${params.fastq}" }
- .set { fastq_files }
-
-process adaptor_removal {
- tag "$reads.baseName"
- publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
- input:
- file reads from fastq_files
-
- output:
- file "*_cut.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
- -o ${reads.baseName}_cut.fastq.gz \
- ${reads} > ${reads.baseName}_report.txt
- """
-}
-
--
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