Public | Automated Build

Last pushed: a month ago
Short Description
DELLY workflow used in the PPCG consortium, developed at bric.ku.dk
Full Description

Delly workflow using bio_pype

This docker images is used to run delly pipeline as it is implemented in the computerome HPC system

DELLY

DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions, insertions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

Panel of normal

The collection of SVs from 1000 genomes project and PCAWG is available from synapse

synapse get syn9934121

The tar.gz archive needs to be provided as local file in the Dockstore json.
After downloading the file, for example in the /tmp folder, edit the sv-collection entry ion the json as:

"sv-collection": {
    "path": "/tmp/svCallCollectionsPCAWG.tar.gz",
    "class": "File"
},

or provide the path of the file in the run script arguments if run interactively from a Docker container

GC content wiggle file

The gc_wig parameter in the cwl consists in a GC content wiggle file. The parameter is optional, if it is not provided the workflow would generate a wig file using the provided fasta reference file.
A gc wiggle of the human genome hs37d5, is available at bricweb

Once the file has been dowloaded, it can be added in the Dockstore.json file as following:

  "gc_wig": {
    "path": "/tmp/genome.gc.wig.gz",
    "class": "File"
  },

Building

You need Docker installed in order to perform this build.

    cd finsen_delly_workflow
    docker build -t bric-embl_delly_workflow:latest .

Local test:

    dockstore tool launch --entry Dockstore.cwl --local-entry --json sample_configs.local.json
Docker Pull Command
Owner
weischenfeldt

Comments (0)