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Verified Commit 600ee64e authored by Laurent Modolo's avatar Laurent Modolo
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hisat2: change report file name

parent 30bc832d
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......@@ -76,9 +76,9 @@ process mapping_fastq {
-x ${index_id} \
-1 ${reads[0]} \
-2 ${reads[1]} 2> \
${file_prefix}_ht2_mapping_report_tmp.txt \
${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \
${file_prefix}_ht2_mapping_report_tmp.txt \
${file_prefix}_ht2_mapping_report.txt \
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
${file_prefix}_ht2_mapping_report.txt
......@@ -92,7 +92,7 @@ process mapping_fastq {
-p ${task.cpus} \
-x ${index_id} \
-U ${reads} 2> \
${file_prefix}_ht2_mapping_report_tmp.txt \
${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \
${file_prefix}_ht2_mapping_report.txt \
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
......
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