From 911287b288a517c7da46c550cabe34af5b2a82ae Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 24 Aug 2018 16:05:24 +0200
Subject: [PATCH] training_dataset.nf: fix filtering for single-end
---
src/training_dataset.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/training_dataset.nf b/src/training_dataset.nf
index 017f94b..58c9bbb 100644
--- a/src/training_dataset.nf
+++ b/src/training_dataset.nf
@@ -13,10 +13,10 @@ output:
- sort fastq
example for paired-end data:
-./nextflow src/training_dataset.nf -c src/training_dataset.config --fasta "data/genome.fa" --fastq_paired "data/BNLN16.R{1,2}*" --chromosome "X" --start 5305683 --stop 5333928 -resume
+./nextflow src/training_dataset.nf -c src/training_dataset.config --fasta "data/genome.fa" --fastq_paired "data/*_R{1,2}.fastq.gz" --chromosome "X" --start 5305683 --stop 5333928 -resume
example for single-end data:
-./nextflow src/training_dataset.nf -c src/training_dataset.config --fasta "data/genome.fa" --fastq_single "data/BNLN16.R1*" --chromosome "X" --start 5305683 --stop 5333928 -resume
+./nextflow src/training_dataset.nf -c src/training_dataset.config --fasta "data/genome.fa" --fastq_single "data/*_R1.fastq.gz" --chromosome "X" --start 5305683 --stop 5333928 -resume
*/
@@ -220,7 +220,7 @@ if ( params.fastq_single != "" ) {
set file_id, "*.fastq" into fastq_files_extracted
script:
"""
- samtools fastq -s ${file_id}_S.fastq -f 0x2 ${bam}
+ samtools fastq -0 ${file_id}_S.fastq -F 0x4 ${bam}
"""
}
@@ -237,7 +237,7 @@ if ( params.fastq_single != "" ) {
set file_id, "*_S.bam" into filtered_bam_files
script:
"""
- samtools view -@ ${task.cpus} -hb ${bam} -f 0x2 > ${file_id}_S.bam
+ samtools view -@ ${task.cpus} -hb ${bam} -F 0x4 > ${file_id}_S.bam
"""
}
}
--
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