pacsomatic
Category: life-sciences · License: MIT · Version: 1.2 · Includes scripts
Tags: tumor-normal, somatic variants, nf-core, long-read sequencing, cancer genomics
When to use it
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 triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.Example requests
Ask your agent in plain language, for example:- “do a dry run of pacsomatic on my tumor/normal pair first and tell me what’s missing”
- “I have PacBio HiFi BAMs for patient P017: /data/p017/P017_T.hifi.bam (sample P017_T) and /data/p017/P017_N.hifi.bam (sample P017_N), reference is /ref/GRCh38.fa. Submit it to our Slurm cluster, partition ‘long’, account ‘onc-lab’, output in /scratch/p017_out, and give me the job id. Last time sbatch failed with ‘Invalid account or account/partition combination specified’.”
- “I’ve got long-read tumor and matched normal BAMs for one patient and want somatic variant calls through the nf-core long-read somatic workflow. Can you get everything set up so I can rerun it later exactly the same way?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.