1000RNASEQ chicken ASE: disable bam indexing in splitNCigar to avoid trouble...

1000RNASEQ chicken ASE: disable bam indexing in splitNCigar to avoid trouble with datetime of output file

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 
         """