first commit

README.md

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+word.docx

defaults

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+{   
+    "mixcr_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/mixcr:3",
+    "mixcr_cluster":"OnDemand bcs.b4.3xlarge img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

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+{
+	"{{ project_name }}.sample_id": "{{ sample_id }}",
+	"{{ project_name }}.fastq1": "{{ fastq1 }}",
+	"{{ project_name }}.fastq2": "{{ fastq2 }}",
+	"{{ project_name }}.mixcr_docker": "{{ mixcr_docker }}",
+	"{{ project_name }}.mixcr_cluster": "{{ mixcr_cluster }}",
+	"{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/mixcr.wdl

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+task mixcr{
+    String sample_id
+    File fastq1
+    File fastq2
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir  ${sample_id}_mixcr_output
+        mixcr analyze shotgun --species hs \
+            -t 4 \
+            --starting-material rna \
+            --only-productive ${fastq1} ${fastq2} ${sample_id}_mixcr_output/${sample_id}
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] mixcr_result=glob("${sample_id}_mixcr_output/${sample_id}*")
+    }
+
+}
+
+

workflow.wdl

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+import "./tasks/mixcr.wdl" as mixcr
+workflow {{ project_name }} {
+    String sample_id
+    File fastq1
+    File fastq2
+
+    String mixcr_docker
+    String mixcr_cluster
+    String disk_size
+
+        call mixcr.mixcr as mixcr {
+                input:	
+                sample_id=sample_id,
+                fastq1=fastq1,
+                fastq2=fastq2,
+                docker=mixcr_docker,
+                cluster=mixcr_cluster,
+                disk_size=disk_size
+
+        }
+
+
+}