Merge pull request #4 from d3b-center/bug-fix/mb-update-auotpvs1

🔧 Bug fix auotpvs1

README.md

@@ -1,14 +1,14 @@
 # Pathogenicity Preprocessing Workflow
 
 ## Prequisite
-It is recommended to have first run the [Kids First Germline Annotation Workflow](https://github.com/kids-first/kf-germline-workflow/blob/v0.4.4/docs/GERMLINE_SNV_ANNOT_README.md) first.
+It is recommended to have first run the [Kids First Germline Annotation Workflow](https://github.com/kids-first/kf-germline-workflow/blob/v1.0.0/docs/GERMLINE_SNV_ANNOT_README.md) first.
 
 ## Pathogenicity Preprocessing Workflow
 This workflow uses the prerequisite input to run the InterVar workflow and autoPVS1 tool.
 The major pieces of software being used are:
  - ANNOVAR latest: The software has no versioning, but references do. See `annovar_db` section in [Recommended inputs](#recommended-inputs)
  - InterVar v2.2.1
- - AutoPVS1 v1.0.1: Modified from AutoPVS1 v2.0 to fit annotated KF vcf output. See [README for autoPVS1](https://github.com/d3b-center/D3b-autoPVS1/tree/v1.0.0#readme) for details
+ - AutoPVS1 v2.0.0: Modified from AutoPVS1 v2.0 to fit annotated KF vcf output. See [README for autoPVS1](https://github.com/d3b-center/D3b-autoPVS1/tree/v2.0.0#readme) for details
 ### Recommended inputs:
  - `annovar_db`: ANNOVAR Database with at minimum required resources to InterVar. Need to use [ANNOVAR download commands](https://annovar.openbioinformatics.org/en/latest/user-guide/download/) to get the following:
      ```
@@ -80,4 +80,4 @@ This workflow is a critical component in generating scoring metrics needed to cl
 Documentation for this can be found [here](docs/INTERVAR_WF.md)
 ### AutoPVS1
 An additional pathogenicity scoring tool, run on the VEP-annotated input.
-Documentation for this can be found [here](https://github.com/d3b-center/D3b-autoPVS1/tree/v1.0.0#readme)
+Documentation for this can be found [here](https://github.com/d3b-center/D3b-autoPVS1/tree/v2.0.0#readme)

tools/autopvs1.cwl

@@ -11,7 +11,7 @@ requirements:
     ramMin: 16000
     coresMin: 8
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v1.0.1'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v2.0.0'
 
 baseCommand: []
 arguments:
@@ -35,7 +35,7 @@ arguments:
 inputs:
   autopvs1_db: { type: File, doc: "Annovar Database with at minimum required resources to InterVar", inputBinding: { position: 0 }}
   autopvs1_db_str: { type: 'string?', doc: "Name of dir created when annovar db is un-tarred", inputBinding: { position: 1, prefix: "--data_dir" }, default: "data"}
-  vep_vcf: { type: File, doc: "VEP annotated input file", inputBinding: { position: 2, prefix: "--vep_vcf"} }
+  vep_vcf: { type: File, doc: "VEP annotated input file", inputBinding: { position: 2, prefix: "--vep_vcf"}, secondaryFiles: ['.tbi']}
   genome_version:  { type: ['null', { type: enum, symbols: ["hg38","GRCh38"], name: "genome_version" } ], doc: "Genome reference build version",
     default: "hg38", inputBinding: { position: 2, prefix: "--genome_version" } }
   output_basename: { type: string, doc: "String that will be used in the output filenames" }

workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl

@@ -13,7 +13,7 @@ doc: |-
   The major pieces of software being used are:
    - ANNOVAR latest: The software has no versioning, but references do. See `annovar_db` section in [Recommended inputs](#recommended-inputs)
    - InterVar v2.2.1
-   - AutoPVS1 v1.0.1: Modified from the original to fit annotated KF vcf output. See [README for autoPVS1](https://github.com/d3b-center/D3b-autoPVS1/tree/v1.0.0#readme) for details
+   - AutoPVS1 v2.0.0: Modified from the original to fit annotated KF vcf output. See [README for autoPVS1](https://github.com/d3b-center/D3b-autoPVS1/tree/v2.0.0#readme) for details
   ### Recommended inputs:
    - `annovar_db`: ANNOVAR Database with at minimum required resources to InterVar. Need to use [ANNOVAR download commands](https://annovar.openbioinformatics.org/en/latest/user-guide/download/) to get the following:
        ```
@@ -166,7 +166,7 @@ hints:
 - class: sbg:maxNumberOfParallelInstances
   value: 2
 "sbg:links":
-- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing/releases/tag/v1.0.0'
+- id: 'https://github.com/d3b-center/D3b-Pathogenicity-Preprocessing/releases/tag/v1.0.1'
   label: github-release
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC