Plan and configure nf-core/sarek variant analysis runs from samplesheets.
npx skills add https://github.com/danilomonge/nf-claw --skill sarek
Please help me install this Agent Skill. Skill: sarek Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/sarek Command: npx skills add https://github.com/danilomonge/nf-claw --skill sarek
nf-core/sarek automates germline and somatic variant analysis so researchers do not need to manually assemble complex Nextflow commands, parameter sets, and reference inputs for every sequencing project.
Ask for a complete nf-core/sarek run plan for my samplesheet, including the required parameters, recommended step, and the exact nfclaw command for my chosen sequencing scenario.
High-intent search queries and answers about installing and using this skill.
To configure a tumor-normal sequencing run, provide a validated samplesheet and required parameters to define the workflow. The Skill orchestrates execution planning by constraining inputs and flags against a pinned release schema.
You can plan germline and somatic variant calling workflows for whole-genome, whole-exome, targeted, tumor-normal, and tumor-only sequencing runs. The Skill validates samplesheet inputs and required parameters for each scenario.
Yes, nf-core/sarek validates samplesheet inputs, required parameters, allowed values, and file formats before the run starts. It relies on a pinned release schema to constrain inputs and ensure output contracts are met.
Request a complete run plan for your samplesheet to receive the exact Nextflow command. The Skill generates execution configurations including required parameters, recommended steps, and tool-specific run flags.
Yes, nf-core/sarek supports targeted, whole-exome, and whole-genome sequencing workflows. The Skill validates allowed values and run configurations for each sequencing scenario before execution.
Run planning fails parameter validation when inputs do not match the pinned release schema. The Skill strictly validates required flags, allowed values, and file formats before generating an execution plan.
danilomongeRun the nf-core hgtseq pipeline from a samplesheet with validated parameters.
provectusGuide construction of genomics pipelines for alignment, variant calling, and annotation.
kiryteoAutomate nf-core pipeline execution for RNA-seq, WGS/WES, and ATAC-seq data.
MubasherMohammedConverts whole-genome sequencing data into polygenic risk scores via nf-core/sarek and bcftools VCF QC.
