merge metadata changes and updated raw imports from develop to master (…

…#91) * Add metadata to workflows published on dockstore (#89) * add metadata to u_of_michigan_aligner.wdl * add metadata to FunctionalEquivalence.wdl * add metadata for topmed_freeze3_calling.wdl * add metadata sbg-alignment-cwl/topmed-alignment.cwl * add metadata functional equivalent aligner: /topmed-cwl/workflow/alignment_workflow.cwl * add metadata to topmed_freeze3_calling.cwl * add metadata topmed_variant_calling_pipeline.cwl * update raw imports for 1.32.0 release (#90)
DataBiosphere · Mar 11, 2019 · 6478d5d · 6478d5d
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diff --git a/CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.wdl b/CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.wdl
@@ -1,5 +1,5 @@
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.wdl" as f1
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/CRAM-no-header-md5sum/checker/CRAM_md5sum_checker.wdl" as f2
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/CRAM-no-header-md5sum/md5sum/CRAM_md5sum.wdl" as f1
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/CRAM-no-header-md5sum/checker/CRAM_md5sum_checker.wdl" as f2
 
 workflow CRAMMd5sumChecker {
   File inputCRAMFile

diff --git a/aligner/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl b/aligner/functional-equivalence-checker/checker-workflow-wrapping-alignment-workflow.wdl
@@ -1,5 +1,5 @@
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl" as TopMed_aligner
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/functional-equivalence-checker/topmed-alignment-checker.wdl" as checker
 
 workflow checkerWorkflow {
   Int expectedNumofReads

diff --git a/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl b/aligner/functional-equivalence-wdl/FunctionalEquivalence.wdl
@@ -273,6 +273,11 @@ workflow PairedEndSingleSampleWorkflow {
     File output_cram_index = ConvertToCram.output_cram_index
     File output_cram_md5 = ConvertToCram.output_cram_md5
   }
+  meta {
+              author : "Ruchi Munshi"
+              email : "[email protected]"
+              description: "A WDL workflow based on the [CCDG pipeline standards](https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md) for processing high-throughput sequencing data."
+    }
 }
 
 # TASK DEFINITIONS

diff --git a/aligner/sbg-alignment-cwl/topmed-alignment.cwl b/aligner/sbg-alignment-cwl/topmed-alignment.cwl
@@ -4,6 +4,8 @@ id: topmed_alignment
 doc: >-
   A CWL wrapper of the TopMed alignment workflow described here:
   https://github.com/statgen/docker-alignment
+  Tool Author: Hyun Min Kang ([email protected]) and Adrian Tan ([email protected])
+  Wrapper Author: Marko Zecevic ([email protected])
 label: TOPMed Alignment
 $namespaces:
   sbg: 'https://sevenbridges.com'

diff --git a/aligner/topmed-cwl/workflow/alignment_workflow.cwl b/aligner/topmed-cwl/workflow/alignment_workflow.cwl
@@ -12,6 +12,9 @@ doc: |
       - reads are provided in query-sorted order
       - all reads must have an RG tag
     - Reference genome must be Hg38 with ALT contigs
+'dct:creator':
+  'foaf:mbox': 'mailto:yilinxu@uchicago.edu'
+  'foaf:name': Yilin Xu
 
 class: Workflow
 id: alignment_pipeline

diff --git a/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker.wdl b/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker.wdl
@@ -1,5 +1,5 @@
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl" as TopMed_aligner
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker_calculation.wdl" as checker
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl" as TopMed_aligner
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker_calculation.wdl" as checker
 
 workflow checkerWorkflow {
   String docker_image

diff --git a/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl b/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl
@@ -216,6 +216,11 @@ workflow TopMedAligner {
       File aligner_output_cram = PostAlign.output_cram_file
       File aligner_output_crai = PostAlign.output_crai_file
   }
+  meta {
+            author : "Walt Shands"
+            email : "[email protected]"
+            description: "This is the workflow WDL for the [TOPMed/University of Michigan alignment pipeline](https://github.com/statgen/docker-alignment)"
+  }
 }
 
   task PreAlign {

diff --git a/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl b/variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl
@@ -2,6 +2,8 @@ class: CommandLineTool
 cwlVersion: v1.0
 id: >-
   vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/topmed_freeze3_calling/25
+doc: >-
+  This is the CWL wrapper for U of Michigan's [TOPMed Freeze 3a Variant Calling Pipeline](https://github.com/statgen/topmed_freeze3_calling)
 baseCommand: []
 inputs:
   - format: 'BAI,CRAI'
@@ -545,4 +547,7 @@ $namespaces:
 'sbg:projectName': TOPMed Freeze 3a Variant Calling Pipeline
 'sbg:createdBy': mikojicic
 'sbg:modifiedBy': vladimir_obucina
+'dct:creator':
+  'foaf:mbox': 'mailto:[email protected]'
+  'foaf:name': Vladimir Obucina
 'sbg:validationErrors': []
diff --git a/variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl b/variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl
@@ -2,6 +2,8 @@ class: Workflow
 cwlVersion: v1.0
 id: >-
   vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/topmed-variant-calling-pipeline-cwl1/17
+doc: >-
+    This is the CWL wrapper for U of Michigan's [TOPMed Freeze 3a Variant Calling Pipeline](https://github.com/statgen/topmed_freeze3_calling)
 label: TOPMed Variant Calling Pipeline CWL1
 inputs:
   - id: reference
@@ -150,4 +152,7 @@ requirements:
     - class: InlineJavascriptRequirement
 $namespaces:
   sbg: 'https://sevenbridges.com'
+'dct:creator':
+  'foaf:mbox': 'mailto:[email protected]'
+  'foaf:name': Vladimir Obucina
 
diff --git a/variant-caller/variant-caller-wdl-checker/topmed_freeze3_calling_checker.wdl b/variant-caller/variant-caller-wdl-checker/topmed_freeze3_calling_checker.wdl
@@ -1,5 +1,5 @@
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl" as TopMed_variantcaller
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/variant-caller/variant-caller-wdl-checker/topmed-variantcaller-checker.wdl" as checker
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl" as TopMed_variantcaller
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/variant-caller/variant-caller-wdl-checker/topmed-variantcaller-checker.wdl" as checker
 
 workflow checkerWorkflow {
   File inputTruthVCFFile

diff --git a/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl b/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl
@@ -1,4 +1,4 @@
-import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.30.0/variant-caller/variant-caller-wdl/calculate_contamination.wdl" as getDNAContamination
+import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.32.0/variant-caller/variant-caller-wdl/calculate_contamination.wdl" as getDNAContamination
 
 
 ## This is the U of Michigan variant caller workflow WDL for the workflow code located here:
@@ -443,6 +443,11 @@ workflow TopMedVariantCaller {
   output {
       File topmed_variant_caller_output = variantCalling.topmed_variant_caller_output_file
   }
+  meta {
+      author : "Walt Shands"
+      email : "[email protected]"
+      description: "This is the workflow WDL for U of Michigan's [TOPMed Freeze 3a Variant Calling Pipeline](https://github.com/statgen/topmed_freeze3_calling)"
+   }
 }