Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and

pacsomatic When to use Use [scripts/run pacsomatic.py](scripts/run pacsomatic.py) to prepare one matched PacBio HiFi tumor/normal pair, generate a samplesheet and reproducible launch artifacts, and launch locally or submit the Nextflow driver to a scheduler. The pipeline realigns input BAMs; this helper targets unaligned HiFi BAMs and optional PacBio .pbi indexes. Do not substitute short reads or treat a BAM filename as evidence of platform, matched identity, or methylation information. The reviewed upstream dev commit is 24c84cb371b0339c1d65a4de9451671945e19772 . GitHub had no releases or tags on 2026 10 01, despite the internal manifest saying 1.0.0 . The helper pins that commit by default for nf core/pacsomatic ; it does not invent a release tag. This is a source reviewed development workflow, not a clinically validated assay. See [references/pacsomatic guide.md](references/pacsomatic guide.md) for sources and scientific checks. Workflow 1. Obtain distinct tumor and normal BAM paths, patient ID, distinct sample IDs, output directory, and exactly one reference mode: fasta or genome . IDs and BAM/PBI/FASTA paths must have no whitespace. Local inputs must be nonempty regular files. Remote BAM/PBI/FASTA URIs are passed through without downloading or authenticating; use managed filesystem/cloud credentials, never embed secrets or signed URLs in generated files. 2. Confirm PacBio HiFi read groups and sample identity from acquisition metadata; confirm that MM/ML modification tags needed for methylation have been retained. Verify reference sequence/contig compatibility for every annotation resource. 3. Generate artifacts with dry run . This performs helper checks and writes files, but does not invoke the pipeline, validate BAM contents, check remote availability, resolve every pipeline parameter, or verify biological suitability. Missing runtime tools are warnings here. dry run cannot be combined with run / submit , cloning, or environment creation. 4. Review samplesheet, generated params YAML, script, pipeline revision, profiles, and branch specific resources/skips. Existing artifacts require explicit overwrite ; input files can never be artifact targets. config.yaml is an operator reference, not an automatically loaded configuration file. 5. For execution, select the actual runtime with use current path or an existing conda env . Load cluster modules before invoking the helper; module load only repeats those commands in the generated script. No Conda YAML is bundled; creating an environment needs conda env file explicitly. 6. Use run only for requested execution. For HPC, distinguish the outer launcher scheduler ( executor ) from Nextflow's per task process.executor , configured by a site profile or nextflow config . Driver CPU/memory requests do not constrain task resources. Read [references/config and output.md](references/config and output.md). 7. Report artifact paths, revision, checks/warnings, run type, submission ID if present, and a concrete next QC or failure triage step. Scheduler acceptance is not pipeline completion. Keep the output directory and work/cache state stable for resume ; scripts run with the output directory as their cwd. Examples Run these from the repository root. Paths and site settings are illustrative ; local tests use synthetic placeholders only, not human genomic data. After reviewing artifacts, a Slurm launch can use the same inputs plus the following options (replace dry run with run ): Those resources are for the driver, assuming the reviewed infrastructure config sets process.executor = 'slurm' and suitable task queue/resources. The helper normalizes 48:00 to Slurm 48:00:00 (48 hours). Do not add a sanger profile unless actually using that institution's LSF infrastructure. Custom pipeline parameters go in params file ; infrastructure goes in nextflow config ( c ). The helper's explicit input/outdir/reference options win over params file values. extra args is tokenized and shell quoted, but cannot override these managed inputs/configuration options. Keep paths inside external params/config files absolute because the launcher cwd is the outdir. Verification and references The standard library suite checks local artifact behavior, path protections, CLI modes, runtime failures and mocked scheduler submissions. Native Nextflow checks use a tiny local workflow; they do not establish that pacsomatic's full containerized scientific pipeline succeeds on a given dataset or cluster. [Operator playbook](references/agent playbook.md) [Configuration, scheduler and output contracts](references/config and output.md) [Upstream sources and scientific checks](references/pacsomatic guide.md)