Run the nf-core/mag metagenomics pipeline from samplesheet to annotated outputs.
npx skills add https://github.com/danilomonge/nf-claw --skill mag
Please help me install this Agent Skill. Skill: mag Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/mag Command: npx skills add https://github.com/danilomonge/nf-claw --skill mag
This Skill removes the complexity of running nf-core/mag by turning a large metagenomics workflow into a guided, validated run with the right inputs, parameters, and provenance captured automatically.
Ask the assistant to run the mag metagenomics pipeline with my samplesheet, output directory, and preferred profile, then generate the command and validate the required parameters.
High-intent search queries and answers about installing and using this skill.
To assemble and annotate metagenomes, this Skill guides the nf-core/mag pipeline from validated samplesheet inputs to assembled contigs, binned genomes, and taxonomic profiles. It automates module wiring to produce MultiQC summaries and bin QC reports.
Running an nf-core/mag metagenomics pipeline requires a strictly validated CSV samplesheet and schema-backed parameters. You must provide input read data, an output directory, and a preferred execution profile to generate the validated run command.
Yes, hybrid metagenomic data can be used for binning and taxonomic profiling. The workflow processes short-read, long-read, and hybrid inputs, applying bin refinement and virus detection to generate assembled contigs and annotated bins.
Reproducible provenance is tracked by recording the pinned pipeline release, exact commit, and run command. This ensures safe execution and allows researchers to reliably rerun or audit metagenomics workflows.
Metagenomics pipeline runs fail fast on invalid inputs due to strict schema-backed parameter validation. This mechanism checks provided CSV samplesheet paths, flags, and values before execution to prevent downstream processing errors.
The best way to handle bin refinement and virus detection in Nextflow is using a guided workflow that applies strict validation. This approach manages read preprocessing and genome annotation automatically within the nf-core framework.
danilomongeOrchestrate nf-core/metapep pipeline runs for reproducible epitope predictions from metagenomic samples.
fmschulzDetect viral contigs, classify taxonomy, and assess genome quality with geNomad, vConTACT3, and CheckV.
danilomongeRun the nf-core/callingcards pipeline for Calling Cards sequencing data.
rhysnewellAutomate metagenomic assembly, binning, annotation, and dereplication workflows.
