Nextflow
Writes, runs and debugs Nextflow and nf-core pipelines.
Install
gh skill install K-Dense-AI/scientific-agent-skills nextflow
Any reproducible bioinformatics workflow work: running or debugging an nf-core pipeline, writing DSL2 modules, or configuring HPC/cloud executors.
- Author
- K-Dense Inc.
- License
- Apache-2.0
Splits the work into two paths from the start: running an existing nf-core pipeline and debugging a failed resume, or writing DSL2 processes, channels and modules from scratch. Executor and container configuration spans local runs, SLURM and other HPC schedulers, and AWS, Google, Azure or Kubernetes backends — same pipeline, different profile. Reproducibility gets concrete handling through per-task containers, pinned pipeline revisions, a pinned engine version and resume caching. Module and subworkflow testing goes through nf-test under nf-core linting conventions.
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