Run nf-core/cutandrun workflows for CUT&RUN, CUT&Tag, and TIPseq data.
npx skills add https://github.com/danilomonge/nf-claw --skill cutandrun
Please help me install this Agent Skill. Skill: cutandrun Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/cutandrun Command: npx skills add https://github.com/danilomonge/nf-claw --skill cutandrun
This Skill removes the guesswork from running nf-core/cutandrun by turning a complex sequencing analysis pipeline into a reproducible, parameter-safe workflow for CUT&RUN, CUT&Tag, and TIPseq data.
Ask the assistant to run the cutandrun Skill on your samplesheet and output directory, then choose the appropriate profile and any required pipeline version or reference settings.
High-intent search queries and answers about installing and using this skill.
CUT&RUN analysis pipelines can be run end-to-end by providing a samplesheet and output directory, then selecting the appropriate profile to execute alignment, deduplication, normalization, peak calling, and reporting automatically.
Yes, the nf-core cutandrun pipeline supports CUT&Tag and TIPseq sequencing data alongside CUT&RUN, processing all three assay types through the same validated workflow for alignment, peak calling, and QC.
Reproducible peak calling results are ensured by release pinning, which locks the pipeline to a specific validated version and records provenance so outputs can be rerun and audited consistently.
Yes, validated pipeline parameters and upstream references for outputs, tools, and constraints are required inputs, ensuring the CUT&RUN workflow preserves pinned versions and provenance throughout execution.
Samplesheet validation occurs at the start of the CUT&RUN pipeline to verify input data integrity before proceeding to alignment, deduplication, normalization, and peak calling stages.
CUT&RUN pipeline runs produce QC summaries, peak calling outputs, normalization data, and publication-ready reports, with provenance tracking for reproducible protein-DNA interaction analysis.
ammawlaProcess CUT&RUN and CUT&Tag sequencing data with SEACR peak calling.
MDheweiAnnotate ATAC-seq or ChIP-seq peaks with genomic context and QC metrics.
EpiphyticRun nf-core Nextflow pipelines for RNA-seq, variant, and ATAC-seq analyses.
ammawlaAutomates CUT&RUN and CUT&Tag sequencing analysis from raw FASTQ reads to peak calls with Nextjob workflows.
