nextflow
Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.
- Version
- 1.2
- License
- Apache-2.0
Pinned to revision df088027ff23, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/nextflow/SKILL.md
- skills/nextflow/references/configuration.md
- skills/nextflow/references/containers.md
- skills/nextflow/references/developing.md
- skills/nextflow/references/language.md
- skills/nextflow/references/nf-core-tools.md
- skills/nextflow/references/running-pipelines.md
- skills/nextflow/references/testing.md
Every link opens the file at its source, pinned to the revision this page describes.