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Verified Commit 801d4f6a authored by Laurent Modolo's avatar Laurent Modolo
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bwa: fix bug :46

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src/nf_modules/bwa/main.nf
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...@@ -43,7 +43,7 @@ if (file_id.containsKey('library')) { ...@@ -43,7 +43,7 @@ if (file_id.containsKey('library')) {
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina" bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
""" """
bwa mem -t ${task.cpus} \ bwa mem -t ${task.cpus} \
-R '${params.bwa_mem_R}' \ -R '${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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