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Verified Commit 3cfd27b2 authored by Laurent Modolo's avatar Laurent Modolo
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bwa: fix index variable

parent 7d92ce73
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......@@ -66,7 +66,7 @@ bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumi
bwa mem -t ${task.cpus} \
${params.mapping_fastq} \
-R '${bwa_mem_R}' \
${index_id} ${reads[0]} ${reads[1]} 2> \
${index} ${reads[0]} ${reads[1]} 2> \
${file_prefix}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
"""
......@@ -75,7 +75,7 @@ ${index_id} ${reads[0]} ${reads[1]} 2> \
bwa mem -t ${task.cpus} \
${params.mapping_fastq} \
-R '${bwa_mem_R}' \
${index_id} ${reads} 2> \
${index} ${reads} 2> \
${file_prefix}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
"""
......
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