first commit

schema.json

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+{
+  "formMode":"batch",
+  "fields":[
+    {
+      "tmplType":"sample_id",
+      "type":"number",
+      "label":"Sample ID",
+      "name":"sample_id",
+      "question":"How many samples? For auto generating sample id.",
+      "placeholder":"How many samples? For auto generating sample id.",
+      "model":"sample_id",
+      "disabled":false,
+      "min":1,
+      "max":10,
+      "config":{
+        "rules":[{"type":"number","required":true,"message":"Please input a number."}]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"Read1 Files",
+      "model":"read1",
+      "readOnly":false,
+      "multiple":true,
+      "filterType":"fastq|fastq.gz|fq|fq.gz",
+      "placeholder":"Select files for read1.",
+      "config":{
+        "rules":[
+          {
+            "type":"array",
+            "required":true,
+            "message":"Please select files for read1."
+          }
+        ]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"Read2 Files",
+      "model":"read2",
+      "readOnly":false,
+      "multiple":true,
+      "filterType":"fastq|fastq.gz|fq|fq.gz",
+      "placeholder":"Select files for read2.",
+      "config":{
+        "rules":[
+          {
+            "type":"array",
+            "required":true,
+            "message":"Please select files for read2."
+          }
+        ]
+      }
+    },
+    {
+      "tmplType":"actions",
+      "buttons":[
+        {"type":"cancel","buttonType":"default","buttonLabel":"Previous Step"},
+        {
+          "type":"submit",
+          "buttonType":"primary",
+          "buttonLabel":"Next Step",
+          "validate":true
+        }
+      ]
+    }
+  ]
+}

tasks/fusioncatcher.wdl

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+task fusioncatcher{
+    String sample_id
+    File fastq1
+    File fastq2
+    File database_dir
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir ./output/
+
+        /software/fusioncatcher/bin/fusioncatcher \
+            -d ${database_dir} \
+            -p 4 \
+            -i ${fastq1},${fastq2} \
+            --output ./output
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] fusioncatcher_result=glob("./output/*.txt")
+        Array[File] fusioncatcher_zip=glob("./output/*.zip")
+        Array[File] fusioncatcher_log=glob("./output/*.log")
+        Array[File] fusioncatcher_vcf=glob("./output/*.vcf")
+    }
+
+}
+
+