From c4c472cc937ed9e74fb3b3504c749d58ee20e6e1 Mon Sep 17 00:00:00 2001
From: mherbett <marion.herbette@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:51:09 +0000
Subject: [PATCH] RNASEQ.nf : add block fo bedtools (do no emove channel)
---
src/RNASeq.nf | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index 57fa500..df39196 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -70,4 +70,44 @@ UrQt --t 20 --m ${task.cpus} --gz \
"""
}
+/*
+* bedtools :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/* fasta extraction */
+
+params.fastq = "$baseDir/data/fasta/*.fasta"
+params.bed = "$baseDir/data/annot/*.bed"
+
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+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: ${params.bed}" }
+ .set { bed_files }
+
+process fasta_from_bed {
+ tag "${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