From d37507059dd41977c83cbcb613e18f34357b4657 Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Tue, 11 Jun 2019 12:12:30 +0200
Subject: [PATCH] 1000RNASEQ_chicken/ASE : correction of phASER command line
---
Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk b/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk
index b239bb5..fc7ac09 100644
--- a/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk
+++ b/Snakemake/1000RNASeq_chicken/ASE/rules/ASE_counter.smk
@@ -55,5 +55,5 @@ rule phASER:
paired_option = lambda wildcards : '1' if len(table[table['sample_name'] == wildcards.sample]['forward_read']) == len(table[table['sample_name'] == wildcards.sample]['reverse_read'].dropna()) else '0'
shell:
"""
- python2.7 phaser.py --vcf {input.vcf} --bam {input.bam} --sample {wildcards.sample} --threads {threads} --o 'Results/Counter/{wildcards.sample}_phASER --paired_end {params.paired_option} --baseq {params.baseQuality} --mapq {params.mappingQuality}
+ python2.7 phaser.py --vcf {input.vcf} --bam {input.bam} --sample {wildcards.sample} --threads {threads} --o Results/Counter/{wildcards.sample}_phASER --paired_end {params.paired_option} --baseq {params.baseQuality} --mapq {params.mappingQuality}
"""
--
GitLab