更新 'tasks/suppa2.wdl'

2

tasks/suppa2.wdl

@@ -12,16 +12,13 @@ task suppa2{
 	
         set -o pipefail
         set -e
-        echo ${sample_id} > test.txt
-        echo ${fastq1} >> test.txt
-        echo ${fastq2} >>test.txt
-        echo ${suppa2_database} >>test.txt
 
-#         /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
-#        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}
+
+        /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
+        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}
 
     >>>
 	
@@ -33,11 +30,10 @@ task suppa2{
     }
 
     output {
-         File suppa2_events = "test.txt"
-#        File suppa2_events = "${sample_id}_events.psi"
-#        File suppa2_isoform = "${sample_id}_events.psi"
-#        File TPM = "${sample_id}_iso_tpm.txt"
-#        File formatted_TPM = "${sample_id}_iso_tpm_formatted.txt"
+        File suppa2_events = "${sample_id}_events.psi"
+        File suppa2_isoform = "${sample_id}_events.psi"
+        File TPM = "${sample_id}_iso_tpm.txt"
+        File formatted_TPM = "${sample_id}_iso_tpm_formatted.txt"
     }
 
 }