From d28f6bf430ec7ede43c4b91ac11070b6322fa717 Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:50:25 +0000
Subject: [PATCH] RNAseq.nf : add bedtools block
---
src/RNAseq.nf | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 37f5bde..a679273 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -1,11 +1,23 @@
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq" /* we can use now a param -fastq to specify where are fastq files. this path is the default path */
+params.fasta = "$baseDir/data/fasta/*.fasta"
+params.bed = "$baseDir/data/annot/*.bed"
log.info "fastq files : ${params.fastq}"
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_files }
+Channel
+ .fromPath( params.bed )
+ .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+ .set { bed_files }
process adaptor_removal {
tag "$pair_id"
@@ -45,4 +57,22 @@ UrQt --t 20 --m ${task.cpus} --gz \
"""
}
+process fasta_from_bed {
+ tag "${bed.baseName}"
+ cpus 4
+ publishDir "results/fasta/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files
+ file bed from bed_files
+
+ output:
+ file "*_extracted.fasta" into fasta_files_extracted
+
+ script:
+"""
+bedtools getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
--
GitLab