Description

• Since the addition of the workflow for VCF input, the workflow selection logic was broken leading to pipeline failure if a single sSNV caller was requested. This is now fixed.
• NFTest paths were updated to finish accommodation of new tool versions and to simplify and remove redundant paths to equivalent files.

Closes #313

Testing Results

• NFTest
  • output: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/8.1.0/sfitz-fix-single-tool-runs
  • logs: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/8.1.0/sfitz-fix-single-tool-runs/log*
  • cases:
    • a_mini-all-tools-std-input
    • a_mini-all-tools-vcf-input
    • a_mini-somaticsniper
    • a_mini-strelka2
    • a_mini-mutect2
    • a_mini-muse
    • a_mini-mutect2-multiple-samples
    • a_mini-mutect2-tumor-only

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 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 A-mini sample.