From f885908c909caee564a03ad97f69091e81c693aa Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Tue, 29 Aug 2023 13:41:03 -0400 Subject: [PATCH 1/2] :wrench: fix missing secondary file :oencil: update docs with new versions --- README.md | 4 ++-- tools/autopvs1.cwl | 4 ++-- workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 7082058..2e4d23f 100644 --- a/README.md +++ b/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: ``` diff --git a/tools/autopvs1.cwl b/tools/autopvs1.cwl index 926b590..02e987d 100644 --- a/tools/autopvs1.cwl +++ b/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" } diff --git a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl index 313f25b..904f269 100644 --- a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl +++ b/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: ``` From 850310fee5654014b4414018531e323d3d9d4731 Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Tue, 29 Aug 2023 13:45:29 -0400 Subject: [PATCH 2/2] :pencil: bump versions reflecting bug fix --- README.md | 2 +- workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 2e4d23f..b33390e 100644 --- a/README.md +++ b/README.md @@ -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) \ No newline at end of file +Documentation for this can be found [here](https://github.com/d3b-center/D3b-autoPVS1/tree/v2.0.0#readme) \ No newline at end of file diff --git a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl index 904f269..bd26e18 100644 --- a/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl +++ b/workflows/d3b-diskin-pathogenicity-preprocess-wf.cwl @@ -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