Devin McCabe dpmccabe
dpmccabe
/ cnv_common_tasks.wdl
Created
February 25, 2025 15:27
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| version 1.0 | |
| task PreprocessIntervals { | |
| input { | |
| File? intervals | |
| File? blacklist_intervals | |
| File ref_fasta | |
| File ref_fasta_fai | |
| File ref_fasta_dict | |
| Int? padding |
dpmccabe
/ ensembl_vep-v113.Dockerfile
Created
April 30, 2025 19:30
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| # based on https://github.com/Ensembl/ensembl-vep/blob/release/112/docker/Dockerfile | |
| # but with everything installed as root (to make it easier to run on files in /cromwell_root) | |
| ARG BRANCH=release/113 | |
| ################################################### | |
| # Stage 1 - docker container to build ensembl-vep # | |
| ################################################### | |
| FROM ubuntu:22.04 AS builder | |
| # Update aptitude and install some required packages |
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| [ | |
| { | |
| "name": "age", | |
| "type": "integer", | |
| "description": "age of donor at time of sampling", | |
| "required": false, | |
| "unique": false | |
| }, | |
| { | |
| "name": "age_category", |
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