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Verified Commit c6865206 authored by Laurent Modolo's avatar Laurent Modolo
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hisat2: remove samtools report

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src/nf_modules/hisat2/main.nf
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− 9
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...@@ -77,10 +77,8 @@ process mapping_fastq { ...@@ -77,10 +77,8 @@ process mapping_fastq {
-1 ${reads[0]} \ -1 ${reads[0]} \
-2 ${reads[1]} 2> \ -2 ${reads[1]} 2> \
${file_prefix}_ht2_mapping_report.txt \ ${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \ | samtools view -@ ${task.cpus} -bS - \
${file_prefix}_ht2_samtools_view_report.txt \ | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
${file_prefix}_ht2_samtools_sort_report.txt
if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1 exit 1
...@@ -93,11 +91,8 @@ process mapping_fastq { ...@@ -93,11 +91,8 @@ process mapping_fastq {
-x ${index_id} \ -x ${index_id} \
-U ${reads} 2> \ -U ${reads} 2> \
${file_prefix}_ht2_mapping_report.txt \ ${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \ | samtools view -@ ${task.cpus} -bS - \
${file_prefix}_ht2_samtools_view_report.txt \ | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
${file_prefix}_ht2_samtools_sort_report.txt
if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1 exit 1
fi fi
......
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