Agent skill
nextflow-pipelines-step-3-run-test-profile
Sub-skill of nextflow-pipelines: Step 3: Run Test Profile.
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/step-3-run-test-profile
SKILL.md
Step 3: Run Test Profile
Step 3: Run Test Profile
Validates environment with small data. MUST pass before real data.
nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output
| Pipeline | Command |
|---|---|
| rnaseq | nextflow run nf-core/rnaseq -r 3.22.2 -profile test,docker --outdir test_rnaseq |
| sarek | nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek |
| atacseq | nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq |
Verify:
ls test_output/multiqc/multiqc_report.html
grep "Pipeline completed successfully" .nextflow.log
If test fails, see references/troubleshooting.md.
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