Run the nf-core hgtseq pipeline from a samplesheet with validated parameters.
npx skills add https://github.com/danilomonge/nf-claw --skill hgtseq
Please help me install this Agent Skill. Skill: hgtseq Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/hgtseq Command: npx skills add https://github.com/danilomonge/nf-claw --skill hgtseq
nf-core hgtseq automates a complex horizontal gene transfer analysis workflow so researchers do not have to manually stitch together preprocessing, alignment, taxonomic screening, and reporting steps.
Ask the agent to run hgtseq on my samplesheet with the required taxonomy ID, output directory, and reference databases, then produce the pipeline results and report.
High-intent search queries and answers about installing and using this skill.
To run the hgtseq pipeline, provide a validated samplesheet, required taxonomy ID, reference databases, and output directory. The Skill executes the nf-core workflow, validates inputs, and generates standardized results with MultiQC reporting.
Horizontal gene transfer analysis identifies genetic material movement between organisms using next-generation sequencing data. The nf-core hgtseq pipeline automates preprocessing, alignment, taxonomic screening, and reporting steps into a reproducible workflow.
The Skill supports release-pinned reruns by fixing the selected nf-core hgtseq pipeline version and recording runtime environment provenance. This captures the exact execution context needed to reproduce results consistently.
Yes, the Skill supports reproducible execution on both local and containerized Nextflow setups. It records provenance for the selected pipeline version and runtime environment to ensure consistent results across different configurations.
No, the Skill automatically validates the samplesheet and required parameters before execution. It enforces schema-constrained flags and allowed values, ensuring inputs meet the pipeline requirements without manual preprocessing.
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