[Fix Bug] to_json filter doesn't exist & imporve schema.

inputs

@@ -6,7 +6,7 @@
   "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
   "{{ project_name }}.idx": "{{ idx }}",
   "{{ project_name }}.gtf": "{{ gtf }}",
-  "{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}",
+  "{{ project_name }}.disk_size": "{{ disk_size if disk_size else 200}}",
   "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
   "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
   "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",
@@ -30,7 +30,7 @@
   "{{ project_name }}.count_docker": "{{ count_docker }}",
   "{{ project_name }}.count_cluster": "{{ count_cluster }}",
   "{{ project_name }}.count_length": "{{ count_length }}",
-  "{{ project_name }}.trim_adapter":  {{ trim_adapter }},
-  "{{ project_name }}.pre_alignment_qc": {{ pre_alignment_qc }},
-  "{{ project_name }}.qualimap_qc": {{ qualimap_qc }}
+  "{{ project_name }}.trim_adapter":  {{ trim_adapter | tojson }},
+  "{{ project_name }}.pre_alignment_qc": {{ pre_alignment_qc | tojson }},
+  "{{ project_name }}.qualimap_qc": {{ qualimap_qc | tojson }}
 }

schema.json

@@ -1,138 +1,163 @@
 {
-  "formMode":"batch",
-  "fields":[
+  "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": "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":[
+      "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."
+            "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":[
+      "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."
+            "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": "FastqScreen Conf File",
+      "model": "fastq_screen_conf",
+      "readOnly": false,
+      "multiple": false,
+      "filterType": "conf",
+      "placeholder": "Select file for fastq screen.",
+      "config": {
+        "initialValue": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
+        "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":[
+      "tmplType": "file",
+      "label": "References of Fastq Screen",
+      "model": "screen_ref_dir",
+      "readOnly": false,
+      "filterType": "",
+      "multiple": false,
+      "placeholder": "Select directory for Fastq Screen References.",
+      "config": {
+        "initialValue": "oss://pgx-reference-data/fastq_screen_reference/",
+        "rules": [
           {
-            "required":true,
-            "message":"Select directory for Fastq Screen References."
+            "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": "Index Directory",
+      "model": "idx",
+      "readOnly": false,
+      "filterType": "",
+      "multiple": false,
+      "placeholder": "Select directory for idx.",
+      "config": {
+        "initialValue": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
+        "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": "file",
+      "label": "GTF File",
+      "model": "gtf",
+      "readOnly": false,
+      "multiple": false,
+      "filterType": "gtf",
+      "placeholder": "Select file for gtf.",
+      "config": {
+        "initialValue": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
+        "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":[
+      "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."
+            "type": "string",
+            "required": false,
+            "message": "Please input an index prefix."
           }
         ]
       }
     },
     {
-      "tmplType":"actions",
-      "buttons":[
-        {"type":"cancel","buttonType":"default","buttonLabel":"Previous Step"},
+      "tmplType": "actions",
+      "buttons": [
+        {
+          "type": "cancel",
+          "buttonType": "default",
+          "buttonLabel": "Previous Step"
+        },
         {
-          "type":"submit",
-          "buttonType":"primary",
-          "buttonLabel":"Next Step",
-          "validate":true
+          "type": "submit",
+          "buttonType": "primary",
+          "buttonLabel": "Next Step",
+          "validate": true
         }
       ]
     }