bio-workflow-management-nextflow-pipelines

bio-workflow-management-nextflow-pipelines is a Bioinformatics & life sciences skill for AI agents, published by GPTomics in the bioSkills repository on GitHub. Skillspace rates bio-workflow-management-nextflow-pipelines C (73/100) and it passed the safety scan; the rating is based on static analysis only.

Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. Use when deciding channel/dataflow (Nextflow) vs rule-based (Snakemake) authoring; wiring queue vs value channels and fixing shared-reference exhaustion with .first(); composing DSL2 modules and subworkflows with take/main/emit; selecting container/conda profiles and pinning images by digest for portability across local/SLURM/LSF/AWS Batch/Google Batch/Kubernetes executors; diagnosing why -resume misses the cache (nondeterministic input order, mtime on network filesystems, mutable :latest tags) with cache 'lenient' and -dump-hashes; managing work/ vs publishDir and dynamic retry escalation; and choosing whether to adopt an nf-core community pipeline or author from scratch.

Grade

C

Quality

73 / 100

Safety

Passed

GitHub stars

1,025

Unproven: rated by static analysis only, not yet compared head-to-head.

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