Generate validated execution plans for nf-core/demultiplex runs.
npx skills add https://github.com/danilomonge/nf-claw --skill demultiplex
Please help me install this Agent Skill. Skill: demultiplex Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/demultiplex Command: npx skills add https://github.com/danilomonge/nf-claw --skill demultiplex
This Skill removes the guesswork from running nf-core/demultiplex by turning a complex sequencing workflow into a validated, reproducible run plan with the right inputs, flags, and release-specific guidance.
Use the demultiplex skill to run nf-core/demultiplex on your samplesheet with the correct release, required parameters, and output directory.
High-intent search queries and answers about installing and using this skill.
You run nf-core demultiplex by submitting a structured Illumina sequencing samplesheet and optional flowcell details to generate a validated, provenance-safe Nextflow execution plan with correct parameters and output directories.
Demultiplexing in Nextflow separates pooled Illumina sequencing reads into individual samples based on barcode indices. You need it when processing raw sequencing data from a shared flowcell before downstream bioinformatics analysis.
Yes, the nf-core demultiplex pipeline enforces strict parameter validation, allowed-value enforcement, and release-pinned pipeline versions to ensure provenance-safe command generation for Illumina sequencing runs.
Yes, you can pin a specific nf-core demultiplex release version. The pipeline supports release-pinned reruns and pipeline version checks to guarantee reproducible sequencing demultiplexing workflows.
The best way to avoid invalid flags is to use a validated execution plan that applies strict parameter validation and allowed-value enforcement, surfacing parameter constraints before Nextflow launch.
Nf-core demultiplex runs fail with mismatched pipeline versions when release pins are not enforced. Applying release-pinned pipeline version checks ensures compatibility and provenance-safe command generation.
danilomongeRun the nf-core hgtseq pipeline from a samplesheet with validated parameters.
jaechang-hitsProcess SAM, BAM, and CRAM alignment files with samtools.
danilomongeExecute the nf-core/atacseq workflow for ATAC-seq alignment, peak calling, QC, and differential analysis.
danilomongeRun the nf-core/ampliseq pipeline for amplicon sequencing analysis.
