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Verified Commit e801efee authored by Laurent Modolo's avatar Laurent Modolo
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bwa: fix previous commit

parent 70a181f4
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......@@ -35,10 +35,11 @@ process mapping_fastq {
tuple val(file_id), path("${file_id}_bwa_report.txt"), emit: report
script:
if (file_id.containsKey('library')):
if (file_id.containsKey('library')) {
library = file_id.library
else:
} else {
library = file_id
}
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
"""
bwa mem -t ${task.cpus} \
......
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