Nextflow Pipelines Step 2 Select Pipeline

Sub-skill of nextflow-pipelines: Step 2: Select Pipeline.

vamseeachanta Updated

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Step 2: Select Pipeline

Step 2: Select Pipeline

DECISION POINT: Confirm with user before proceeding.

Data Type Pipeline Version Goal
RNA-seq rnaseq 3.22.2 Gene expression
WGS/WES sarek 3.7.1 Variant calling
ATAC-seq atacseq 2.1.2 Chromatin accessibility

Auto-detect from data:

python scripts/detect_data_type.py /path/to/data

For pipeline-specific details:

  • references/pipelines/rnaseq.md
  • references/pipelines/sarek.md
  • references/pipelines/atacseq.md

vamseeachanta/workspace-hub/tree/main/.agents/skills/_archive/science/bio-research/nextflow-pipelines/step-2-select-pipeline commit ac8cf619da

Frequently asked questions

npx skillmds@latest add vamseeachanta/nextflow-pipelines-step-2-select-pipeline