From aafb78a0c5535b473b19bd1b68f7b8952a04b574 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 31 May 2018 17:16:33 +0200
Subject: [PATCH] cutadapt.nf: adaptator trimming code for paired and
single-ends
---
src/nf_modules/cutadapt/cutadapt.nf | 67 +++++++++++++++++++++++++++++
1 file changed, 67 insertions(+)
create mode 100644 src/nf_modules/cutadapt/cutadapt.nf
diff --git a/src/nf_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
new file mode 100644
index 0000000..7273441
--- /dev/null
+++ b/src/nf_modules/cutadapt/cutadapt.nf
@@ -0,0 +1,67 @@
+/*
+* cutadapt :
+* Imputs : fastq files
+*/
+
+/* Illumina adaptor removal
+
+/*
+* 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: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$pair_id"
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ set "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_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: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$reads.baseName"
+
+ 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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