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Verified Commit ade97af3 authored by Laurent Modolo's avatar Laurent Modolo
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bwa: fix bwa_mem_R call

parent 449693e2
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...@@ -38,7 +38,7 @@ process mapping_fastq { ...@@ -38,7 +38,7 @@ process mapping_fastq {
script: script:
""" """
bwa mem -t ${task.cpus} \ bwa mem -t ${task.cpus} \
-R ${bwa_mem_R} \ -R ${params.bwa_mem_R} \
${index_id} ${reads[0]} ${reads[1]} 2> \ ${index_id} ${reads[0]} ${reads[1]} 2> \
${file_id}_bwa_report.txt | \ ${file_id}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam
......
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