--- name: pacsomatic-5425319387be description: 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. license: MIT compatibility: Requires Python 3.10+ for the standard-library helper. Execution requires Bash, Nextflow >=24.04.2, a compatible Java runtime (current Nextflow supports Java 17-26), the selected container runtime and optionally a scheduler. Network access is needed for uncached pipeline code, plugins, references and containers. metadata: version: "1.4" skill-author: Beifang Niu contributors: Haidong, Wenchao upstream-pipeline: https://github.com/nf-core/pacsomatic upstream-revision: "24c84cb371b0339c1d65a4de9451671945e19772" last-reviewed: "2026-10-01" --- # 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. ```bash 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`): ```text --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. ## Verification and references ```bash 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. - [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) --- Source attribution: boisenoise Original project: https://github.com/boisenoise/skills-collections/blob/aa13ba97f9669f891f0ae560f5e0924aefd62e9a/skills/kdense-pacsomatic/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2026 Beifang Niu Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: boisenoise Original project: https://github.com/boisenoise/skills-collections/blob/aa13ba97f9669f891f0ae560f5e0924aefd62e9a/skills/kdense-pacsomatic/SKILL.md Attribution basis: Source repository record Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences Roles: Clinical Research, Data Scientist, Researcher Specialties: Backend, Frontend, Git, Testing Tools: Nextflow, Nf Core Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: a9c57717188d16f6125b7a0740f2f9ebc6024e47533382693bacc6b06e2c2aeb