From 59ba3f4b8c4d6246fe889cc052dd90d3b47df418 Mon Sep 17 00:00:00 2001
From: hpolvech <helene.polveche@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:46:13 +0000
Subject: [PATCH] RNASeq.nf:Bedtools
---
src/RNASeq.nf | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index c96a9e7..eb6d3a6 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -50,3 +50,50 @@ UrQt --t 20 --m ${task.cpus} --gz \
"""
}
+
+/*
+* bedtools :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/* fasta extraction */
+
+params.fasta = "$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
+"""
+}
+
+
+
+
+
+
--
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