Screen assembled contigs for functional genes with nf-core/funcscan workflows.
npx skills add https://github.com/danilomonge/nf-claw --skill funcscan
Please help me install this Agent Skill. Skill: funcscan Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/funcscan Command: npx skills add https://github.com/danilomonge/nf-claw --skill funcscan
This Skill helps you run the nf-core/funcscan pipeline correctly without guessing flags, so you can screen assembled contigs and related sequence inputs for functional genes with reproducible, validated parameters.
Ask the assistant to run the funcscan skill on your samplesheet, choose the output directory, and execute the pipeline with the appropriate profile for your environment.
High-intent search queries and answers about installing and using this skill.
You can screen assembled contigs for functional genes by running the nf-core/funcscan pipeline with a validated samplesheet containing FASTA and annotation inputs. This coordinates antimicrobial peptide, antibiotic resistance, biosynthetic gene cluster, and CAZyme screening from one command.
The best way to run antimicrobial peptide and antibiotic resistance screening is through the nf-core/funcscan workflow, which uses release-pinned Nextflow execution and strict parameter validation to ensure reproducible pipeline runs with documented input and output contracts.
Yes, you can use a samplesheet with GFF and GBK files for biosynthetic gene cluster screening. The pipeline accepts samplesheets with contigs, proteins, GFFs, or GBKs to produce module outputs plus a MultiQC summary.
Yes, you need to pin a specific Nextflow release to reproduce functional gene screening results. The skill uses release-pinned Nextflow execution and documents required inputs, outputs, and parameter constraints for dependable, reproducible runs.
Functional gene screening requires strict parameter validation to ensure reproducible pipeline runs. Without validated parameters, the nf-core/funcscan workflow cannot guarantee consistent analysis outputs or dependable module results across different execution environments.
Screening contigs for CAZymes and biosynthetic gene clusters requires properly formatted samplesheets with FASTA and annotation inputs. Limitations arise if input contracts are not documented or if Nextflow execution is not release-pinned for reproducible runs.
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