Commit 1e004588 authored by Eric CHARPENTIER's avatar Eric CHARPENTIER 🐍
Browse files

added read group in bam files

parent 1ab964e9
......@@ -223,7 +223,7 @@ rule star_PE:
output: OUTPUTDIR+"/Samples/{sampleName}/STAR/{sampleName}Aligned.sortedByCoord.out.bam"
params: cpu=config["align-cpu"]
shell: """
STAR --runThreadN {params.cpu} --genomeDir {GENOMEDIR} --readFilesCommand zcat --outFileNamePrefix {OUTPUTDIR}/Samples/{wildcards.sampleName}/STAR/{wildcards.sampleName} --readFilesIn {input.R1} {input.R2} --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 6
STAR --runThreadN {params.cpu} --genomeDir {GENOMEDIR} --readFilesCommand zcat --outFileNamePrefix {OUTPUTDIR}/Samples/{wildcards.sampleName}/STAR/{wildcards.sampleName} --readFilesIn {input.R1} {input.R2} --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 6 --outSAMattrRGline ID:"{wildcards.sampleName}" SM:"{wildcards.sampleName}" LB:"{wildcards.sampleName}" CN:"PFBirdNantes"
"""
......
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