From 4c942973d26fdd6e6fd5c2a601de344277c8a446 Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Wed, 19 Jun 2019 17:21:21 +0200
Subject: [PATCH] 1000RNASEQ chicken ASE: disable bam indexing in splitNCigar
to avoid trouble with datetime of output file
---
Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk b/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
index 053841c..9b9ad02 100644
--- a/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
+++ b/Snakemake/1000RNASeq_chicken/ASE/rules/STAR.smk
@@ -189,7 +189,7 @@ rule SplitNCigarReads:
idx = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.fa.fai',
dict = 'Results/genomeMasked/' + os.path.splitext(os.path.basename(config['fasta_ref']))[0] + '_masked.dict',
bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bam",
- bai = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bai"
+ bai = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq.bam.bai"
output:
bam = "Results/STAR_Aln_2/{sample}_rg_genomic{properlyPaired}rmdup_uniq_split.bam"
params:
@@ -197,6 +197,6 @@ rule SplitNCigarReads:
jar=find_jar("GenomeAnalysisTK.jar")
shell:
"""
- java -Xmx{params.mem} -jar {params.jar} -T SplitNCigarReads -R {input.fasta} -I {input.bam} -o {output.bam} -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
+ java -Xmx{params.mem} -jar {params.jar} -T SplitNCigarReads -R {input.fasta} -I {input.bam} -o {output.bam} --disable_bam_indexing -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
"""
--
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