Prepare and launch nf-core/pacsomatic workflows for matched tumor and normal PacBio HiFi samples. Generate sample sheets and launch files from unaligned BAM inputs, run local checks, submit cluster launchers, and troubleshoot startup failures.
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.
Review the instructions the agent will receive before you install.
Use 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 for sources
and scientific checks.
--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.--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.--overwrite; input files can never be artifact targets. config.yaml is an
operator reference, not an automatically loaded configuration file.--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.--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.--resume; scripts run with the output directory as their cwd.Run these from the repository root. Paths and site settings are illustrative; local tests use synthetic placeholders only, not human genomic data.
python skills/pacsomatic/scripts/run_pacsomatic.py \
--tumor-bam /data/P001_T.bam --normal-bam /data/P001_N.bam \
--patient-id P001 --tumor-sample-id P001_T --normal-sample-id P001_N \
--outdir /results/P001 --fasta /refs/GRCh38.fa \
--profile apptainer --use-current-path --dry-run
After reviewing artifacts, a Slurm launch can use the same inputs plus the
following options (replace --dry-run with --run):
--executor slurm --queue compute --project my_account
--cpus 2 --memory-gb 8 --walltime 48:00
--nextflow-config /configs/slurm.config --overwrite --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.
uv run skills-ref validate skills/pacsomatic
python tests/run_all.py --isolated pacsomatic
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.
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