Nextflow Pipelines Step 3 Run Test Profile

Sub-skill of nextflow-pipelines: Step 3: Run Test Profile.

vamseeachanta Updated

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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.


vamseeachanta/workspace-hub/tree/main/.agents/skills/_archive/science/bio-research/nextflow-pipelines/step-3-run-test-profile commit 8bddebbd97

Frequently asked questions

npx skillmds@latest add vamseeachanta/nextflow-pipelines-step-3-run-test-profile