Update Delly v1.2.9

[Faizal-Eeman]

Description

Update Delly v1.2.9

Closes #28

Testing Results

Docker Image Testing

• I have tested the Docker image with the docker run command as described below.

Test the Docker image with at least one sample. Verify the new Docker image works using:

docker run -u $(id -u):$(id -g) –w <working-directory> -v <directory-you-want-to-mount>:<how-you-want-to-mount-it-within-the-docker> --rm <docker-image-name> <command-to-the-docker-with-all-parameters>

My command:

docker build --no-cache --progress=plain -t delly:v1.2.9 . 2> build.log

docker run -it --rm -u $(id -u):$(id -g) delly:v1.2.9 bash

$ delly
**********************************************************************
Program: Delly
This is free software, and you are welcome to redistribute it under
certain conditions (BSD License); for license details use '-l'.
This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'.

Delly (Version: 1.2.9)
Contact: Tobias Rausch ([email protected])
**********************************************************************

Usage: delly <command> <arguments>

Short-read SV calling:
    call         discover and genotype structural variants
    merge        merge structural variants across VCF/BCF files and within a single VCF/BCF file
    filter       filter somatic or germline structural variants

Long-read SV calling:
    lr           long-read SV discovery

Copy-number variant calling:
    cnv          discover and genotype copy-number variants
    classify     classify somatic or germline copy-number variants

Checklist

Formatting

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have set up or verified the branch protection rule following the github standards before opening this pull request.

File Updates

• I have ensured that the version number update follows the versioning standards.

• I have updated the version number in the Dockerfile, README.md and metadata.yaml files.

• I have updated the dependencies and added my name to the maintainer list in the Dockerfile.

• I have updated the feature changes in the README.md (optional).

• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

GitHub Packages Auto Build Rules

• I have not manually pushed this Docker image to the uclahs-cds container registry (ghcr.io/uclahs-cds) on GitHub.

• I have updated the image_name in the metadata.yaml which is required by GitHub action to automatically build and push the image.

[Faizal-Eeman]

build log - /hot/software/image/docker-Delly/Docker/development/1.2.9/build.log

[yashpatel6]

Looks good!