Move to null instead of string null; include hisat2 for RNA-seq

- SevenBridges now supports standard null so move to that approach for representing None values. - Fixes currently broken RNA-seq workflow by adding hisat2 tarball.
bcbio · Aug 12, 2018 · e06975a · e06975a
1 parent 4369465
commit e06975a
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Showing 96 changed files with 897 additions and 1,161 deletions.
diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json
@@ -26,19 +26,19 @@
             "class": "File",
             "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
         },
-        "null"
+        null
     ],
     "config__algorithm__coverage_interval": [
-        "null",
-        "null"
+        null,
+        null
     ],
     "config__algorithm__effects": [
         "False",
         "False"
     ],
     "config__algorithm__ensemble": [
-        "null",
-        "null"
+        null,
+        null
     ],
     "config__algorithm__exclude_regions": [
         [],
@@ -111,14 +111,14 @@
             "class": "File",
             "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf"
         },
-        "null"
+        null
     ],
     "config__algorithm__validate_regions": [
         {
             "class": "File",
             "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
         },
-        "null"
+        null
     ],
     "config__algorithm__variant_regions": [
         {
@@ -301,8 +301,8 @@
         }
     ],
     "genome_resources__variation__encode_blacklist": [
-        "null",
-        "null"
+        null,
+        null
     ],
     "genome_resources__variation__esp": [
         {
@@ -349,12 +349,12 @@
         }
     ],
     "genome_resources__variation__lcr": [
-        "null",
-        "null"
+        null,
+        null
     ],
     "genome_resources__variation__polyx": [
-        "null",
-        "null"
+        null,
+        null
     ],
     "genome_resources__variation__train_hapmap": [
         {
@@ -569,8 +569,8 @@
         "Test2"
     ],
     "rgnames__lb": [
-        "null",
-        "null"
+        null,
+        null
     ],
     "rgnames__pl": [
         "illumina",
@@ -589,7 +589,7 @@
         "Test2"
     ],
     "vrn_file": [
-        "null",
-        "null"
+        null,
+        null
     ]
 }
diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl
@@ -53,7 +53,6 @@ inputs:
   type:
     items:
     - 'null'
-    - string
     - items:
       - 'null'
       - string
@@ -168,7 +167,6 @@ inputs:
     items:
     - File
     - 'null'
-    - string
     type: array
 - id: reference__snpeff__hg19
   type:
@@ -183,7 +181,6 @@ inputs:
     items:
     - File
     - 'null'
-    - string
     type: array
 - id: config__algorithm__aligner
   type:
@@ -219,7 +216,6 @@ inputs:
     items:
     - File
     - 'null'
-    - string
     type: array
 - id: genome_resources__aliases__human
   type:
@@ -310,10 +306,7 @@ inputs:
   type:
     items:
     - 'null'
-    - string
-    - items:
-      - 'null'
-      - string
+    - items: 'null'
       type: array
     type: array
 - id: reference__rtg

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl
@@ -100,7 +100,6 @@ inputs:
   type:
     items:
     - 'null'
-    - string
     - items:
       - 'null'
       - string
@@ -156,7 +155,6 @@ outputs:
       - name: config__algorithm__adapters
         type:
         - 'null'
-        - string
         - items:
           - 'null'
           - string

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/batch_for_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
@@ -96,14 +96,12 @@ inputs:
           type:
           - File
           - 'null'
-          - string
         - name: reference__snpeff__hg19
           type: File
         - name: config__algorithm__validate_regions
           type:
           - File
           - 'null'
-          - string
         - name: genome_build
           type: string
         - name: genome_resources__variation__exac
@@ -153,10 +151,7 @@ inputs:
         - name: config__algorithm__exclude_regions
           type:
           - 'null'
-          - string
-          - items:
-            - 'null'
-            - string
+          - items: 'null'
             type: array
         - name: reference__rtg
           type: File
@@ -249,14 +244,12 @@ outputs:
           type:
           - File
           - 'null'
-          - string
         - name: reference__snpeff__hg19
           type: File
         - name: config__algorithm__validate_regions
           type:
           - File
           - 'null'
-          - string
         - name: genome_build
           type: string
         - name: genome_resources__variation__exac
@@ -306,10 +299,7 @@ outputs:
         - name: config__algorithm__exclude_regions
           type:
           - 'null'
-          - string
-          - items:
-            - 'null'
-            - string
+          - items: 'null'
             type: array
         - name: reference__rtg
           type: File

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/batch_for_variantcall.cwl b/gvcf_joint/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
@@ -105,10 +105,7 @@ inputs:
   type:
     items:
     - 'null'
-    - string
-    - items:
-      - 'null'
-      - string
+    - items: 'null'
       type: array
     type: array
 - id: config__algorithm__variant_regions
@@ -128,14 +125,12 @@ inputs:
     items:
     - File
     - 'null'
-    - string
     type: array
 - id: config__algorithm__validate_regions
   type:
     items:
     - File
     - 'null'
-    - string
     type: array
 - id: config__algorithm__tools_on
   type:
@@ -319,14 +314,12 @@ outputs:
           type:
           - File
           - 'null'
-          - string
         - name: reference__snpeff__hg19
           type: File
         - name: config__algorithm__validate_regions
           type:
           - File
           - 'null'
-          - string
         - name: genome_build
           type: string
         - name: genome_resources__variation__exac
@@ -376,10 +369,7 @@ outputs:
         - name: config__algorithm__exclude_regions
           type:
           - 'null'
-          - string
-          - items:
-            - 'null'
-            - string
+          - items: 'null'
             type: array
         - name: reference__rtg
           type: File

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/compare_to_rm.cwl b/gvcf_joint/gvcf-joint-workflow/steps/compare_to_rm.cwl
@@ -101,14 +101,12 @@ inputs:
         type:
         - File
         - 'null'
-        - string
       - name: reference__snpeff__hg19
         type: File
       - name: config__algorithm__validate_regions
         type:
         - File
         - 'null'
-        - string
       - name: genome_build
         type: string
       - name: genome_resources__variation__exac
@@ -158,10 +156,7 @@ inputs:
       - name: config__algorithm__exclude_regions
         type:
         - 'null'
-        - string
-        - items:
-          - 'null'
-          - string
+        - items: 'null'
           type: array
       - name: reference__rtg
         type: File
@@ -260,14 +255,12 @@ outputs:
         type:
         - File
         - 'null'
-        - string
       - name: reference__snpeff__hg19
         type: File
       - name: config__algorithm__validate_regions
         type:
         - File
         - 'null'
-        - string
       - name: genome_build
         type: string
       - name: genome_resources__variation__exac
@@ -317,10 +310,7 @@ outputs:
       - name: config__algorithm__exclude_regions
         type:
         - 'null'
-        - string
-        - items:
-          - 'null'
-          - string
+        - items: 'null'
           type: array
       - name: reference__rtg
         type: File

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl b/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
@@ -91,14 +91,12 @@ inputs:
         type:
         - File
         - 'null'
-        - string
       - name: reference__snpeff__hg19
         type: File
       - name: config__algorithm__validate_regions
         type:
         - File
         - 'null'
-        - string
       - name: genome_build
         type: string
       - name: genome_resources__variation__exac
@@ -148,10 +146,7 @@ inputs:
       - name: config__algorithm__exclude_regions
         type:
         - 'null'
-        - string
-        - items:
-          - 'null'
-          - string
+        - items: 'null'
           type: array
       - name: reference__rtg
         type: File

diff --git a/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
@@ -108,14 +108,12 @@ inputs:
         type:
         - File
         - 'null'
-        - string
       - name: reference__snpeff__hg19
         type: File
       - name: config__algorithm__validate_regions
         type:
         - File
         - 'null'
-        - string
       - name: genome_build
         type: string
       - name: genome_resources__variation__exac
@@ -165,10 +163,7 @@ inputs:
       - name: config__algorithm__exclude_regions
         type:
         - 'null'
-        - string
-        - items:
-          - 'null'
-          - string
+        - items: 'null'
           type: array
       - name: reference__rtg
         type: File