Agent skill
nextflow-pipelines-5a-check-genome-availability
Sub-skill of nextflow-pipelines: 5a. Check genome availability (+2).
Install this agent skill to your Project
npx add-skill https://github.com/vamseeachanta/workspace-hub/tree/main/.claude/skills/_archive/science/bio-research/nextflow-pipelines/5a-check-genome-availability
SKILL.md
5a. Check genome availability (+2)
5a. Check genome availability
python scripts/manage_genomes.py check <genome>
# If not installed:
python scripts/manage_genomes.py download <genome>
Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64-1-1 (yeast), BDGP6 (fly)
5b. Decision points
DECISION POINT: Confirm with user:
- Genome: Which reference to use
- Pipeline-specific options:
- rnaseq: aligner (star_salmon recommended, hisat2 for low memory)
- sarek: tools (haplotypecaller for germline, mutect2 for somatic)
- atacseq: read_length (50, 75, 100, or 150)
5c. Run pipeline
nextflow run nf-core/<pipeline> \
-r <version> \
-profile docker \
--input samplesheet.csv \
--outdir results \
--genome <genome> \
-resume
See sub-skills for full details.
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