first commit

defaults

@@ -0,0 +1,8 @@
+{   
+    "suppa2_GTF":"oss://pgx-reference-data/reference/suppa2/gencode.v37.annotation.gtf",
+    "suppa2_GTF":"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_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

@@ -0,0 +1,11 @@
+{
+    "{{ 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_docker": "{{ suppa2_docker }}",
+    "{{ project_name }}.suppa2_cluster": "{{ suppa2_cluster }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/suppa2.wdl

@@ -0,0 +1,42 @@
+task suppa2{
+    String sample_id
+    File fastq1
+    File fastq2
+    File suppa2_GTF
+    File suppa2_ioe
+    File salmon_index
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        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
+        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 ${sample_id}
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File suppa2_events = "${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"
+    }
+
+}
+
+

workflow.wdl

@@ -0,0 +1,30 @@
+import "./tasks/suppa2.wdl" as suppa2
+
+workflow run_suppa2 {
+    String sample_id
+    File fastq1
+    File fastq2
+    File suppa2_GTF
+    File suppa2_ioe
+    File salmon_index
+
+    String suppa2_docker
+    String suppa2_cluster
+    String disk_size
+
+        call suppa2.suppa2 as suppa2 {
+                input:	
+                sample_id=sample_id,
+                fastq1=fastq1,
+                fastq2=fastq2,
+                suppa2_GTF=suppa2_GTF,
+                suppa2_ioe=suppa2_ioe,
+                salmon_index=salmon_index,
+                docker=suppa2_docker,
+                cluster=suppa2_cluster,
+                disk_size=disk_size
+
+        }
+
+
+}