Runs nf-core/airrflow immune-repertoire analysis from raw reads or assembled data.
npx skills add https://github.com/danilomonge/nf-claw --skill airrflow
Please help me install this Agent Skill. Skill: airrflow Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/airrflow Command: npx skills add https://github.com/danilomonge/nf-claw --skill airrflow
This Skill removes the guesswork from running nf-core/airrflow, helping you analyze immune receptor sequencing data without hunting through docs or inventing flags.
Ask this skill to run nf-core/airrflow on your TSV samplesheet with the desired profile and output directory, and it will produce the correct invocation, validate the parameters, and preserve reproducibility.
High-intent search queries and answers about installing and using this skill.
To run an immune repertoire analysis, provide a valid TSV samplesheet and desired parameters. The skill generates the correct nf-core/airrflow Nextflow command, validates inputs against the schema, and executes the pipeline for reproducible results.
Yes, airrflow supports both bulk and single-cell BCR and TCR workflows. It processes raw reads or assembled AIRR data to perform V(D)J assignment, clonal inference, and lineage reconstruction across various immune receptor sequencing data types.
You need a valid TSV samplesheet, a pinned pipeline version, and schema-validated parameters to start a Nextflow airrflow run. The skill uses these inputs to ensure reproducible execution and standardized output reporting.
The airrflow pipeline handles genotype inference and novel allele detection as part of its broad analysis coverage. It applies these processes to immune repertoire data alongside clonal inference and lineage reconstruction during the Nextflow execution.
The best way to extract AIRR data from RNA-seq reads is using the nf-core/airrflow pipeline. The skill configures the RNA-seq-derived receptor extraction process, ensuring the correct Nextflow command runs with schema-validated parameters for accurate results.
Schema-validated parameters ensure reproducible pipeline execution by preventing invalid configurations. Using a pinned release and provenance capture, the skill keeps your nf-core/airrflow runs consistent and avoids errors from incorrect flags or unsupported settings.
danilomongeRun nf-core/detaxizer to identify and remove target taxa from genomic FASTQ data.
ya-wayAnalyze AIRR-formatted BCR repertoires with Immcantation for SHM, clonal evolution, and lineage reconstruction.
tassiovaleAutomate creation, execution, and debugging of Nextflow workflows.
StarlitnightlyGenerate publication-quality plots with matplotlib and seaborn.
