Execute the nf-core/atacseq workflow for ATAC-seq alignment, peak calling, QC, and differential analysis.
npx skills add https://github.com/danilomonge/nf-claw --skill atacseq
Please help me install this Agent Skill. Skill: atacseq Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/atacseq Command: npx skills add https://github.com/danilomonge/nf-claw --skill atacseq
This Skill removes the manual guesswork from running the nf-core/atacseq workflow by turning a validated samplesheet and parameter set into a reproducible ATAC-seq analysis run with the correct pinned release, outputs, and provenance.
Ask the Skill to run the atacseq pipeline on your samplesheet, confirm the required parameters, and generate a reproducible results directory.
High-intent search queries and answers about installing and using this skill.
To run a reproducible ATAC-seq pipeline, provide a validated CSV samplesheet and configurable parameters to execute the nf-core/atacseq workflow with release-pinned consistency and provenance capture.
End-to-end ATAC-seq data analysis includes sample input validation, alignment, peak calling, quality control, and differential analysis, generating organized results with MultiQC reporting for downstream interpretation.
Yes, a schema-checked samplesheet is required for ATAC-seq peak calling to ensure validated sample inputs and strict parameter compliance before Nextflow execution begins.
Yes, the nf-core atacseq workflow accepts optional reference genomes alongside configurable analysis profiles, allowing customized ATAC-seq alignment and peak calling across supported Nextflow engine versions.
ATAC-seq pipeline results become inconsistent without release-pinned execution, but this workflow tracks the exact atacseq repository release to maintain reproducible outputs and provenance across runs.
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zongtingweiProcess ATAC-seq data into QC metrics, peak calls, and accessible region summaries.
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