pacsomatic
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi
by k-dense-aiFree
Description
pacsomatic is an agent skill for preparing and launching the nf-core pacsomatic workflow, which analyses matched tumour and normal PacBio HiFi genomics data from unaligned BAM files. The skill includes a helper script that prepares one matched tumour and normal pair, generates a samplesheet and reproducible launch files, and then runs the Nextflow driver locally or submits it to a scheduler. The pipeline realigns the input BAM files, and the helper is for unaligned HiFi BAMs and optional PacBio index files. The skill warns against substituting short-read data, and against treating a BAM file name as evidence of the platform, the matched identity or methylation information. The reviewed upstream development commit is pinned by default. GitHub had no releases or tags on 1 October 2026, even though an internal manifest names version 1.0.0, so the helper pins the commit and does not invent a release tag. The skill describes its workflow as a development workflow that has been reviewed against source, not a clinically validated assay. Its guide records the sources and the scientific checks. Use it for research on matched cancer genomes sequenced with PacBio HiFi.…
Highlights
- Prepares matched tumour and normal pairs
- Generates samplesheets and launch files
- Runs locally or submits to a scheduler
- Pinned upstream commit by default
- Research workflow, not a clinical assay
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pacsomatic FAQ
What does it prepare?
A matched tumour and normal PacBio HiFi pair, a samplesheet and reproducible launch files for the nf-core pacsomatic workflow.
What input does it need?
Unaligned HiFi BAM files and optional PacBio index files. The skill advises against substituting short-read data.
Is it clinically validated?
No. The skill describes it as a source-reviewed development workflow, not a clinically validated assay.
Which version does it use?
A pinned upstream development commit, since the project had no releases or tags at review.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pacsomatic.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best pacsomatic alternatives?
Popular alternatives to pacsomatic include gget, biopython and bulk-rnaseq. See all pacsomatic alternatives