subworkflow: fingerprint_gbcms

[anoronh4]

Adding modules and subworkflows for creating a fingerprint vcf using gbcms and then transforming the vcf into a tab-delimited file using a custom script. The tab delimited file is based on the format used in the clinical pipeline. modules also compute contamination, and samples are combined and correlated for confirming that samples match expectations.

fingerprint/vcfparser — Parses a fingerprint VCF file produced by GBCMS into a TSV of locus-level allele counts, genotypes, and VAFs per sample.

fingerprint/combine — Merges per-sample fingerprint TSVs into a single wide table, applying a depth filter and lifting over loci coordinates between hg19 and hg38.

fingerprint/contamination — Calculates major and minor contamination from a pair of tumor/normal fingerprint TSVs.

fingerprint/correlation — Computes pairwise Pearson correlations across all samples in a combined fingerprint table and outputs a heatmap (PDF + interactive HTML), a correlations matrix, and a loci-overlap observations matrix.

fingerprint/mislabels — Flags unexpected sample matches (unrelated samples with suspiciously high correlation) and unexpected mismatches (same-patient samples with suspiciously low correlation) based on patient labels from a sample sheet, using validated thresholds.

PR checklist

• This comment contains a description of changes (with reason).
• Check to see if a nf-core module, or subworkflow is available and usable for your pipeline.
• Feature branch is named feature/<module_name> for modules, or feature/<subworkflow_name> for subworkflows. For modules, if there is a subcommand use: feature/<module_name>/<module_subcommand>.
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs.
• Use nf-core data if possible for nf-tests. If not, use or add test data to mskcc-omics-workflows/test-datasets, following the repository guidelines, for nf-tests. Finally, if neither option is feasible, only add a stub nf-test.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label.
• Use Jfrog if possible to fulfill software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile docker
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularity
    • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda