Add bam index check

[aybeshlikyan]

Checklist

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File Updates

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

• [ ] I have updated the version number/dependencies and added my name to the maintainer list in the Dockerfile.

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• [ ] I have updated the version number and added my name to the contributors list in the metadata.yaml.

• [X] 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.

• [ ] I have drafted the new version release with any additions/changes and have linked the CHANGELOG.md in the release.

Docker Hub Auto Build Rules

• [ ] I have created automated build rules following this page and I have not manually pushed this Docker image to the blcdsdockerregistry on Docker Hub.

Docker Image Testing

• [X] 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:

I created a test directory (/hot/user/abeshlikyan/pipeval_testing_set) that contains:

1. a directory with soft symlinks to both a BAM file and its index (bam_pass/),
2. a directory with a soft symlink to only a BAM file (bam_warn_index_missing/),
3. a directory with soft symlinks to an empty BAM file and its index (bam_fail_empty/), and
4. a directory with an invalid BAM file and index (bam_fail_invalid).

Pull the test image:

docker pull ghcr.io/uclahs-cds/pipeval:abesh-check-bam-index

Runs successfully without outputting a warning:

docker run -it --rm \
-v /hot/user/abeshlikyan/pipeval_testing_set:/tool/test \
-v /hot/resource/pipeline_testing_set/WTS/GRCh37/A/mini/:/hot/resource/pipeline_testing_set/WTS/GRCh37/A/mini \
ghcr.io/uclahs-cds/pipeval:abesh-check-bam-index \
validate test/bam_pass/CPCG0196-F1-A-mini-0-RNA.bam

Runs successfully but outputs a warning about missing BAM index:

docker run -it --rm \
-v /hot/user/abeshlikyan/pipeval_testing_set:/tool/test \
-v /hot/resource/pipeline_testing_set/WTS/GRCh37/A/mini/:/hot/resource/pipeline_testing_set/WTS/GRCh37/A/mini \
ghcr.io/uclahs-cds/pipeval:abesh-check-bam-index \
validate test/bam_warn_index_missing/CPCG0196-F1-A-mini-0-RNA.bam

Fails with error about empty bam file:

docker run -it --rm \
-v /hot/user/abeshlikyan/pipeval_testing_set:/tool/test \
-v /hot/resource/SMC-HET/normal/bams/A-null/:/hot/resource/SMC-HET/normal/bams/A-null/ \
ghcr.io/uclahs-cds/pipeval:abesh-check-bam-index \
validate test/bam_fail_empty/HG002_N_A-null.bam

Fails with error about invalid bam file:

docker run -it --rm \
-v /hot/user/abeshlikyan/pipeval_testing_set:/tool/test \
ghcr.io/uclahs-cds/pipeval:abesh-check-bam-index \
validate test/bam_fail_invalid/invalid.bam

Description

Closes #50. Adds check for BAM index existence.

[aybeshlikyan]

Some notes:

• GItHub Action for auto-building the image will fail because of GCC compiler issue with new(ish) Ubuntu 20.04. I need to manually add the missing dependencies to the Dockerfile to be able to compile pysam.
• The issue with the symlinks that I mentioned during Infra meeting was because I was mounting a volume containing symlinks to the PipeVal container without mounting the actual directory that the symlinks point to. I verified that mounting the original directories allows the tool to resolve the symlinks properly. This shouldn't be an issue when pipeval is run as a process in Nextflow.