Merge http://choppy.3steps.cn/junshang/rnaseq-engineering

manifest.json

@@ -0,0 +1,21 @@
+{
+  "name": "RNA-Seq Pipeline for Production",
+  "short_name": "rnaseq-production",
+  "description": "RNA sequencing analysis pipeline using STAR, HISAT2 etc.",
+  "home": "http://choppy.3steps.cn/junshang/rnaseq-engineering",
+  "hidden": false,
+  "icons": [
+    {
+      "src": "",
+      "type": "image/png",
+      "sizes": "192x192"
+    },
+    {
+      "src": "",
+      "type": "image/png",
+      "sizes": "192x192"
+    }
+  ],
+  "category": "Pipeline",
+  "source": "PGx"
+}

schema.json

@@ -0,0 +1,140 @@
+{
+  "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":100,
+      "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":"file",
+      "label":"FastqScreen Conf File",
+      "model":"fastq_screen_conf",
+      "readOnly":false,
+      "multiple":false,
+      "filterType":"conf",
+      "placeholder":"Select file for fastq screen.",
+      "config":{
+        "rules":[{"required":true,"message":"Please select file for fastq screen."}]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"References of Fastq Screen",
+      "model":"screen_ref_dir",
+      "readOnly":false,
+      "filterType":"",
+      "multiple":false,
+      "placeholder":"Select directory for Fastq Screen References.",
+      "config":{
+        "rules":[
+          {
+            "required":true,
+            "message":"Select directory for Fastq Screen References."
+          }
+        ]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"Index Directory",
+      "model":"idx",
+      "readOnly":false,
+      "filterType":"",
+      "multiple":false,
+      "placeholder":"Select directory for idx.",
+      "config":{
+        "rules":[{"required":true,"message":"Please select directory for idx."}]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"GTF File",
+      "model":"gtf",
+      "readOnly":false,
+      "multiple":false,
+      "filterType":"gtf",
+      "placeholder":"Select file for gtf.",
+      "config":{"rules":[{"required":true,"message":"Please select file for gtf."}]}
+    },
+    {
+      "tmplType":"input",
+      "type":"string",
+      "label":"Index Prefix",
+      "name":"idx_prefix",
+      "placeholder":"Please enter index prefix.",
+      "model":"idx_prefix",
+      "disabled":false,
+      "min":1,
+      "max":100,
+      "config":{
+        "initialValue":"genome_snp_tran",
+        "rules":[
+          {
+            "type":"string",
+            "required":false,
+            "message":"Please input an index prefix."
+          }
+        ]
+      }
+    },
+    {
+      "tmplType":"actions",
+      "buttons":[
+        {"type":"cancel","buttonType":"default","buttonLabel":"Previous Step"},
+        {
+          "type":"submit",
+          "buttonType":"primary",
+          "buttonLabel":"Next Step",
+          "validate":true
+        }
+      ]
+    }
+  ]
+}