nextflow-pipeline

name

nextflow-pipeline

description

Reference for the gbcms Nextflow wrapper — module layout (dna/rna/filter_maf/merge/normalize/pipeline_summary), profiles and SLURM/iris resource routing, the samplesheet schema, multi-BAM merge options, and the places where Nextflow defaults DIVERGE from the CLI defaults. Use when editing anything under nextflow/ or debugging a pipeline run (OOM, queue routing, SLURM retries, output-name collisions).

Nextflow Pipeline

Layout

nextflow/
├── main.nf                       # entry
├── nextflow.config               # params + profiles + resource scopes
├── assets/samplesheet.csv
├── workflows/{dna,rna}.nf
└── modules/local/gbcms/
    ├── dna/main.nf               # GBCMS_DNA
    ├── rna/main.nf               # GBCMS_RNA
    ├── filter_maf/main.nf        # FILTER_MAF (include suffix in output name!)
    ├── merge/main.nf             # MERGE_COUNTS (multi-BAM)
    ├── normalize/main.nf         # standalone normalization
    └── pipeline_summary/main.nf  # PIPELINE_SUMMARY

Resource / HPC notes (hard-won — see recent commits)

• Per-process resource blocks for FILTER_MAF and PIPELINE_SUMMARY exist to prevent OOM. Default memory bumped to 16GB.
• iris profile uses process.queue (not params.partition).
• Dynamic queue routing by resource request; retry on SLURM null exit codes.
• FILTER_MAF output names must include the suffix to avoid collision with multi-BAM samples.

Multi-BAM merge

• merge_counts enables MERGE_COUNTS (requires bam_type in samplesheet).
• merge_add_combined computes simplex_duplex_* columns; merge_legacy_naming uses t_{metric}_{type} (genotype_variants compat).

⚠️ Nextflow vs CLI default divergences (trap)

nextflow.config is not a 1:1 mirror of CLI defaults. Known differences:

• alignment_backend = 'pairhmm' (NF) vs sw (CLI default).
• min_mapq = 20, min_baseq = 20 set explicitly in NF.
• enforce_strandedness = true (NF) — note this is currently a no-op unless gene_strand is populated from the GTF.
• apply_baq = false in config, but RNA relies on the CLI default (on) unless explicitly set — modules pass --apply-baq/--no-baq conditionally.

When changing a CLI default or filter, update nextflow.config in the same change.

Key Files

• nextflow/nextflow.config, nextflow/modules/local/gbcms/*/main.nf
• nextflow/README.md, docs/nextflow/parameters.md