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Unverified Commit e5648eb2 authored by Laurent Modolo's avatar Laurent Modolo
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SNP_calling.nf: change RG tag order

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......@@ -146,8 +146,8 @@ process mapping_fastq {
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--rg-id ${sample_name} \
--rg SM:${sample_name} \
--rg PL:Illumina \
--rg SM:${sample_name} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
......
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