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Add F16 config to support A-full and larger datasets #36

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merged 2 commits into from
Jul 11, 2022

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Faizal-Eeman
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@Faizal-Eeman Faizal-Eeman commented Jul 11, 2022

Description

Added F16 compatibility to the pipeline. A-full dataset and datasets of larger size can be used using F16 configurations.

Closes #34

Testing Results

  • DNA A-full
    • sample: T5.T
    • input csv: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmootor-add-F16-config/input/tumor_control_pair_afull.csv
    • config: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmootor-add-F16-config/config/A-full-hg19.config
    • output: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmootor-add-F16-config/A-full
  • DNA Real Sample
    • sample: ILHNLNEV000001-T001-P01-F
    • input csv: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmootor-add-F16-config/input/tumor_control_pair_ILHNLNEV000001-T001-P01-F.csv
    • config: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmootor-add-F16-config/config/ILHNLNEV000001-T001-P01-F-hg38.config
    • output: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/unreleased/mmootor-add-F16-config/ILHNLNEV000001-T001-P01-F/

Checklist

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

  • I have reviewed the Nextflow pipeline standards.

  • 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](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStanda
    rds-Branchprotectionrule) before opening this pull request.

  • I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is 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.

  • I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

  • I have tested the pipeline on at least one DNA A-mini sample and one A-full sample. The paths to the test config files and output directories were attached above.

@Faizal-Eeman Faizal-Eeman added the enhancement New feature or request label Jul 11, 2022
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@tyamaguchi-ucla tyamaguchi-ucla left a comment

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Looks good!

@Faizal-Eeman Faizal-Eeman merged commit 847ac29 into main Jul 11, 2022
@Faizal-Eeman Faizal-Eeman deleted the mmootor-add-F16-config branch July 11, 2022 23:08
@Faizal-Eeman Faizal-Eeman mentioned this pull request Jul 13, 2022
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Add F16.config
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