second commit

defaults

@@ -1,7 +1,7 @@
 {   
-    "STAR_INDEX_DIR":"oss://pgx-reference-data/reference/arriba/STAR_index_hg38_GENCODE37",
-    "ASSEMBLY_FA":"oss://pgx-reference-data/reference/arriba/hg38.fa",
-    "ANNOTATION_GTF":"oss://pgx-reference-data/reference/arriba/GENCODE37.gtf",
+    "star_index_dir":"oss://pgx-reference-data/reference/arriba/STAR_index_hg38_GENCODE37",
+    "assembly_fa":"oss://pgx-reference-data/reference/arriba/hg38.fa",
+    "annotation_gtf":"oss://pgx-reference-data/reference/arriba/GENCODE37.gtf",
     "disk_size":"200",
     "arriba_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/arriba:2.1.0",
     "arriba_cluster":"OnDemand bcs.a2.3xlarge img-ubuntu-vpc"

inputs

@@ -2,9 +2,9 @@
     "{{ project_name }}.fastq1": "{{ fastq1 }}",
     "{{ project_name }}.fastq2": "{{ fastq2 }}",
     "{{ project_name }}.sample_id": "{{ sample_id }}",
-    "{{ project_name }}.STAR_INDEX_DIR": "{{ STAR_INDEX_DIR }}",
-    "{{ project_name }}.ASSEMBLY_FA": "{{ ASSEMBLY_FA }}",
-    "{{ project_name }}.ANNOTATION_GTF": "{{ ANNOTATION_GTF }}",
+    "{{ project_name }}.star_index_dir": "{{ star_index_dir }}",
+    "{{ project_name }}.assembly_fa": "{{ assembly_fa }}",
+    "{{ project_name }}.annotation_gtf": "{{ annotation_gtf }}",
     "{{ project_name }}.disk_size": "{{ disk_size }}",
     "{{ project_name }}.arriba_docker": "{{ arriba_docker }}",
     "{{ project_name }}.arriba_cluster": "{{ arriba_cluster }}"

tasks/arriba.wdl

@@ -2,9 +2,9 @@ task arriba{
     String sample_id
     File fastq1
     File fastq2
-    File STAR_INDEX_DIR
-    File ASSEMBLY_FA
-    File ANNOTATION_GTF
+    File star_index_dir
+    File assembly_fa
+    File annotation_gtf
 
     String disk_size
     String docker
@@ -16,12 +16,12 @@ task arriba{
         set -e
 
         mkdir ./output/
-        echo ${STAR_INDEX_DIR} >output/a.txt
+        echo ${star_index_dir} >output/a.txt
         echo ${fastq1} >> output/a.txt
         echo ${fastq2} >> output/a.txt
         echo ${sample_id} >> output/a.txt
-        echo ${ASSEMBLY_FA} >> output/a.txt
-        echo ${ANNOTATION_GTF} >> output/a.txt
+        echo ${assembly_fa} >> output/a.txt
+        echo ${annotation_gtf} >> output/a.txt
 
 
 

workflow.wdl

@@ -4,9 +4,9 @@ workflow {{ project_name }} {
     String sample_id
     File fastq1
     File fastq2
-    File STAR_INDEX_DIR
-    File ASSEMBLY_FA
-    File ANNOTATION_GTF
+    File star_index_dir
+    File assembly_fa
+    File annotation_gtf
 
     String disk_size
     String arriba_docker
@@ -18,9 +18,9 @@ workflow {{ project_name }} {
                 sample_id=sample_id,
                 fastq1=fastq1,
                 fastq2=fastq2,
-                STAR_INDEX_DIR=STAR_INDEX_DIR,
-                ASSEMBLY_FA=ASSEMBLY_FA,
-                ANNOTATION_GTF=ANNOTATION_GTF,
+                star_index_dir=star_index_dir,
+                assembly_fa=assembly_fa,
+                annotation_gtf=annotation_gtf,
                 disk_size=disk_size,
                 docker=arriba_docker,
                 cluster=arriba_cluster