diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index d4b917f6b40d77704d06b369d55650dbc2e5d9fa..68a65161a2dd082fad1e164b1b871ff35da17acf 100755 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -121,21 +121,14 @@ process trimData { hostname >>${repRID}.trimData.err ulimit -a >>${repRID}.trimData.err - if [ `nproc` -gt 8 ] - then - ncore=8 - else - ncore=`nproc` - fi - # trim fastqs if [ '${fastq[1]}' == 'null' ] then ends='se' - trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j \${ncore} ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err; + trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err; else ends='pe' - trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j \${ncore} ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err; + trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err; fi """ } \ No newline at end of file