更新 'tasks/suppa2.wdl'

tasks/suppa2.wdl

@@ -12,12 +12,30 @@ task suppa2{
 	
         set -o pipefail
         set -e
-
-        /software/salmon-1.5.2_linux_x86_64/bin/salmon quant -i ${suppa2_database}/gencode.v37.transcripts.salmon.index/ -l ISR --gcBias -1 ${fastq1} -2 ${fastq2} -p 16 -o ./${sample_id}_salmon
-        multipleFieldSelection.py -i ./${sample_id}_salmon/quant.sf -k 1 -f 4 -o ${sample_id}_iso_tpm.txt
+        nt=$(nproc)
+                  
+        /software/salmon-1.5.2_linux_x86_64/bin/salmon quant -i ${suppa2_database}/gencode.v37.transcripts.salmon.index/ \
+                  -l ISR \
+                  --gcBias \
+                  -1 ${fastq1} \
+                  -2 ${fastq2} \
+                  -p $nt \
+                  -o ./${sample_id}_salmon
+                  
+        multipleFieldSelection.py -i ./${sample_id}_salmon/quant.sf \
+                  -k 1 \
+                  -f 4 \
+                  -o ${sample_id}_iso_tpm.txt
+                  
         sed 's@|ENSG.*|@@' ${sample_id}_iso_tpm.txt > ${sample_id}_iso_tpm_formatted.txt
-        suppa.py psiPerEvent -i ${suppa2_database}/gencode.v37.all.events.ioe -e ${sample_id}_iso_tpm_formatted.txt -o ${sample_id}_events
-        suppa.py psiPerIsoform -g ${suppa2_database}/gencode.v37.annotation.gtf  -e ${sample_id}_iso_tpm_formatted.txt  -o ${sample_id}
+          
+        suppa.py psiPerEvent -i ${suppa2_database}/gencode.v37.all.events.ioe \
+          -e ${sample_id}_iso_tpm_formatted.txt \
+          -o ${sample_id}_events
+          
+        suppa.py psiPerIsoform -g ${suppa2_database}/gencode.v37.annotation.gtf \
+          -e ${sample_id}_iso_tpm_formatted.txt \
+          -o ${sample_id}
 
     >>>