remove unneeded input parameters in input jsons

ICGC-TCGA-PanCancer · Sep 30, 2018 · e9ea377 · e9ea377
1 parent 1f3ef40
commit e9ea377
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diff --git a/Dockstore.cwl b/Dockstore.cwl
@@ -205,22 +205,6 @@ doc: |
       "reference_gz": {
         "path": "reference/genome.fa.gz",
         "class": "File"
-      },
-      "merged_output_bam": {
-        "path": "merged_output.bam",
-        "class": "File"
-      },
-      "merged_output_bai": {
-        "path": "merged_output.bam.bai",
-        "class": "File"
-      },
-      "merged_output_unmapped_bam": {
-        "path": "merged_output.unmapped.bam",
-        "class": "File"
-      },
-      "merged_output_unmapped_bai": {
-        "path": "outputmerged_output.unmapped.bam.bai",
-        "class": "File"
       }
     }
     ```

diff --git a/Dockstore_cwl.json b/Dockstore_cwl.json
@@ -47,25 +47,5 @@
     "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz",
     "basename": "genome.fa.gz",
     "class": "File"
-  },
-  "merged_output_unmapped_bai": {
-    "path": "s3://oicr.temp/testing-bwa-workflow/merged_output.unmapped.bam.bai",
-    "basename": "merged_output.unmapped.bam.bai",
-    "class": "File"
-  },
-  "merged_output_bam": {
-    "path": "s3://oicr.temp/testing-bwa-workflow/merged_output.bam",
-    "basename": "merged_output.bam",
-    "class": "File"
-  },
-  "merged_output_unmapped_bam": {
-    "path": "s3://oicr.temp/testing-bwa-workflow/merged_output.unmapped.bam",
-    "basename": "merged_output.unmapped.bam",
-    "class": "File"
-  },
-  "merged_output_bai": {
-    "path": "s3://oicr.temp/testing-bwa-workflow/merged_output.bam.bai",
-    "basename": "merged_output.bam.bai",
-    "class": "File"
   }
 }
diff --git a/Dockstore_cwl2.json b/Dockstore_cwl2.json
@@ -38,21 +38,5 @@
   "reference_gz": {
     "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz",
     "class": "File"
-  },
-  "merged_output_unmapped_bai": {
-    "path": "/mnt/output/testing-bwa-workflow/merged_output.unmapped.bam.bai",
-    "class": "File"
-  },
-  "merged_output_bam": {
-    "path": "/mnt/output/testing-bwa-workflow/merged_output.bam",
-    "class": "File"
-  },
-  "merged_output_unmapped_bam": {
-    "path": "/mnt/output/testing-bwa-workflow/merged_output.unmapped.bam",
-    "class": "File"
-  },
-  "merged_output_bai": {
-    "path": "/mnt/output/testing-bwa-workflow/merged_output.bam.bai",
-    "class": "File"
   }
 }
diff --git a/checker-input-cwl.json b/checker-input-cwl.json
@@ -49,26 +49,6 @@
       "basename": "genome.fa.gz",
       "class":"File"
    },
-   "merged_output_unmapped_bai":{  
-      "path":"s3://oicr.temp/testing-bwa-workflow/merged_output.unmapped.bam.bai",
-      "basename": "merged_output.unmapped.bam.bai",
-      "class":"File"
-   },
-   "merged_output_bam":{  
-      "path":"s3://oicr.temp/testing-bwa-workflow/merged_output.bam",
-      "basename": "merged_output.bam",
-      "class":"File"
-   },
-   "merged_output_unmapped_bam":{  
-      "path":"s3://oicr.temp/testing-bwa-workflow/merged_output.unmapped.bam",
-      "basename": "merged_output.unmapped.bam",
-      "class":"File"
-   },
-   "merged_output_bai":{  
-      "path":"s3://oicr.temp/testing-bwa-workflow/merged_output.bam.bai",
-      "basename": "merged_output.bam.bai",
-      "class":"File"
-   },
    "reference_result_normal_bam":{
       "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/reference_results/hg19.chr22.5x.normal.bam",
       "basename": "reference_results.hg19.chr22.5x.normal.bam",