diff --git a/src/nf_modules/bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf index e92cb3d13bf7f05608a6e128201ddc056da3de8c..a24291670b2e3b67ed874e5b833172bb372cde7d 100644 --- a/src/nf_modules/bowtie/mapping_paired.nf +++ b/src/nf_modules/bowtie/mapping_paired.nf @@ -41,12 +41,13 @@ process mapping_fastq { # reads bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \ -1 ${reads[0]} -2 ${reads[1]} 2> \ -${pair_id}_bowtie_report.txt | \ +${pair_id}_bowtie_report_tmp.txt | \ samtools view -Sb - > ${pair_id}.bam -if grep -q "Error" ${pair_id}_bowtie_report.txt; then +if grep -q "Error" ${pair_id}_bowtie_report_tmp.txt; then exit 1 fi +tail -n 15 ${file_id}_bowtie2_report_tmp.txt > ${file_id}_bowtie2_report.txt """ } diff --git a/src/nf_modules/bowtie2/mapping_single.nf b/src/nf_modules/bowtie2/mapping_single.nf index 1b7954ec174cccd0ad70ee02b79b3fd5b1a91589..a264cb72feb20381d67f91aa17b2c390532d3fe4 100644 --- a/src/nf_modules/bowtie2/mapping_single.nf +++ b/src/nf_modules/bowtie2/mapping_single.nf @@ -35,11 +35,12 @@ process mapping_fastq { """ bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \ -U ${reads} 2> \ -${file_id}_bowtie2_report.txt | \ +${file_id}_bowtie2_report_tmp.txt | \ samtools view -Sb - > ${file_id}.bam -if grep -q "Error" ${file_id}_bowtie2_report.txt; then +if grep -q "Error" ${file_id}_bowtie2_report_tmp.txt; then exit 1 fi +tail -n 15 ${file_id}_bowtie2_report_tmp.txt > ${file_id}_bowtie2_report.txt """ }