From 99a62a30469dd94b0d14e5c69fa4778ec1e28259 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 17 Jan 2020 15:13:33 +0100
Subject: [PATCH] create RNASeq.nf
---
src/RNASeq.nf | 24 ++++++++++++++++++++++++
src/fasta_sampler.nf | 2 +-
2 files changed, 25 insertions(+), 1 deletion(-)
create mode 100644 src/RNASeq.nf
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
new file mode 100644
index 00000000..f78d5c2d
--- /dev/null
+++ b/src/RNASeq.nf
@@ -0,0 +1,24 @@
+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"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ set pair_id, "*_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
+ """
+}
diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
index bd2e5397..d1200ed4 100644
--- a/src/fasta_sampler.nf
+++ b/src/fasta_sampler.nf
@@ -9,7 +9,7 @@ process sample_fasta {
file fasta from fasta_file
output:
-file "sample.fasta" into fasta_sample
+file "*_sample.fasta" into fasta_sample
script:
"""
--
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