second commit

defaults

@@ -1,7 +1,5 @@
 {   
-    "suppa2_GTF":"oss://pgx-reference-data/reference/suppa2/gencode.v37.annotation.gtf",
-    "suppa2_ioe":"oss://pgx-reference-data/reference/suppa2/gencode.v37.all.events.ioe",
-    "salmon_index":"oss://pgx-reference-data/reference/suppa2/gencode.v37.transcripts.salmon.index/",
+    "suppa2_database":"oss://pgx-reference-data/reference/suppa2/",
     "suppa2_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/suppa:2.3",
     "suppa2_cluster":"OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "disk_size":"200",

inputs

@@ -2,9 +2,7 @@
     "{{ project_name }}.sample_id": "{{ sample_id }}",
     "{{ project_name }}.fastq1": "{{ fastq1 }}",
     "{{ project_name }}.fastq2": "{{ fastq2 }}",
-    "{{ project_name }}.suppa2_GTF": "{{ suppa2_GTF }}",
-    "{{ project_name }}.suppa2_ioe": "{{ suppa2_ioe }}",
-    "{{ project_name }}.salmon_index": "{{ salmon_index }}",
+    "{{ project_name }}.suppa2_database": "{{ suppa2_database }}",
     "{{ project_name }}.suppa2_docker": "{{ suppa2_docker }}",
     "{{ project_name }}.suppa2_cluster": "{{ suppa2_cluster }}",
     "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/suppa2.wdl

@@ -2,9 +2,7 @@ task suppa2{
     String sample_id
     File fastq1
     File fastq2
-    File suppa2_GTF
-    File suppa2_ioe
-    File salmon_index
+    File suppa2_database
 	
     String docker
     String cluster
@@ -15,11 +13,11 @@ task suppa2{
         set -o pipefail
         set -e
 
-        /software/salmon-1.5.2_linux_x86_64/bin/salmon quant -i ${salmon_index} -l ISR --gcBias -1 ${fastq1} -2 ${fastq2} -p 16 -o ./${sample_id}_salmon
+        /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_ioe} -e ${sample_id}_iso_tpm_formatted.txt -o ${sample_id}_events
-        suppa.py psiPerIsoform -g ${suppa2_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}
 
     >>>
 	

workflow.wdl

@@ -5,9 +5,7 @@ workflow {{ project_name }} {
     String sample_id
     File fastq1
     File fastq2
-    File suppa2_GTF
-    File suppa2_ioe
-    File salmon_index
+    File suppa2_database
 
     String suppa2_docker
     String suppa2_cluster
@@ -69,9 +67,7 @@ workflow {{ project_name }} {
                 sample_id=sample_id,
                 fastq1=fastp.Trim_R1,
                 fastq2=fastp.Trim_R2,
-                suppa2_GTF=suppa2_GTF,
-                suppa2_ioe=suppa2_ioe,
-                salmon_index=salmon_index,
+                suppa2_database=suppa2_database,
                 docker=suppa2_docker,
                 cluster=suppa2_cluster,
                 disk_size=disk_size