Upstream review and scientific interpretation

Reviewed 2026-10-01 against nf-core/pacsomatic development commit 24c84cb371b0339c1d65a4de9451671945e19772. No GitHub releases or tags existed at review time; internal manifest 1.0.0 is not a published release. The manifest requires Nextflow >=24.04.2 and pins nf-schema 2.3.0. Current Nextflow 26.04.6 was used only for a tiny local launcher smoke test, not the complete pipeline.

Scientific boundaries

• Inputs are PacBio HiFi tumor/normal sequencing BAMs, usually unaligned. Upstream realigns with pbmm2, then sorts/indexes. Coordinate-sorted input and existing BAI/CSI are not requirements of this helper's raw-BAM workflow.
• Match patient/sample identity and provenance independently. Two different paths and labels do not establish a biological match or absence of cross-sample contamination. Record chemistry/instrument/read-quality and relevant read groups.
• PacBio PBI indexes store PacBio-specific per-read information; BAI/CSI index coordinate alignments. Check that an optional PBI is from the same BAM.
• Methylation needs suitable modification tags and the phasing branches; absence of MM/ML evidence must not become an inferred unmethylated result.
• FASTA, caller model, VEP species/assembly/cache, repeats, SV controls, gene annotations, heterozygous-site panel and GC profiles must agree with the intended assembly/contigs. GRCh38 is an iGenomes key, not an exhaustive specification of all analysis resources. hg38 and GRCh38 are not blindly interchangeable resource names.
• Tumor purity, coverage, normal contamination, ploidy and calling thresholds affect sensitivity and false positives. Successful completion does not establish clinical validity, somatic truth or an interpretable HRD estimate.
• The paired workflow combines tumor/normal records by patient. The helper intentionally generates only one pair; multiple normals/tumors need an explicit pairing design, not duplicated rows that silently create extra combinations.

Branch-specific configuration

Use the pinned parameter schema and source to choose resources/skips. In the reviewed code, VEP needs vep_assembly and vep_species; clonality checks name heterozygous_sites, gc_profile, and ensembl_data_dir; WES CNVkit needs cnv_target_bed. Missing resources may warn, skip or fail downstream. Methylation needs phasing, and signature/HRD branches depend on relevant SNV/SV results. Do not present the minimal generated params YAML as sufficient for every branch.

Retain pipeline revision, Nextflow/Java versions, configs, actual container/tool versions, BAM/reference/resource checksums, samplesheet and parameters. Upstream loads nf-core/configs from a mutable branch by default; pin custom_config_version in your params file for stronger reproducibility and review external assets. The helper doesn't fetch or validate those resources or institutional credentials.

Official sources checked

• Pipeline usage
• Current parameters
• Output guide
• Release listing
• Pinned manifest and runtime profiles
• Pinned samplesheet schema
• Pinned parameter schema
• Pinned workflow and pairing
• Pinned parameter/sample checks
• Nextflow installation and Java compatibility
• Nextflow executor selection
• Nextflow command line
• Slurm sbatch
• Nextflow LSF memory conventions
• Nextflow PBS Pro
• Nextflow SGE
• Sanger-specific profile
• PacBio BAM metadata and modification tags
• PacBio PBI specification
• IBM LSF runtime limit
• IBM LSF memory-unit examples

There is no PACS/DICOM API or hosted service client in this skill. Its network interfaces are upstream Git/Nextflow fetches and remote input URIs; the helper implements no HTTP request body, authentication, response or pagination contract. Local artifacts/mocked submissions are tested separately from those external services. No human genomic data, production scheduler or full pipeline was used.