Skills Marketplace

Overview

BioContext7 skills are pre-built workflow templates that encode best practices for common bioinformatics tasks. Each skill combines tool discovery, pipeline generation, and validation into a single command.

Available Skills

RNA-seq Analysis

bc7 skill run rna-seq --input ./fastq/ --target nextflow

Generates a complete RNA-seq pipeline:

• Quality control (FastQC, MultiQC)
• Adapter trimming (Trim Galore)
• Alignment (STAR)
• Quantification (featureCounts)
• Differential expression (DESeq2)

Variant Calling

bc7 skill run variant-calling --input ./bam/ --target nextflow

Generates a variant calling pipeline:

• BAM preprocessing (Picard MarkDuplicates)
• Variant calling (GATK HaplotypeCaller)
• Variant filtering (GATK VQSR)
• Annotation (SnpEff)

ChIP-seq Peak Calling

bc7 skill run chip-seq --input ./fastq/ --target snakemake

Generates a ChIP-seq analysis pipeline:

• Read alignment (Bowtie2)
• Peak calling (MACS2)
• Motif analysis (HOMER)
• Quality metrics (deepTools)

Metabolomics

bc7 skill run metabolomics --input ./mzml/ --target nextflow

Generates a metabolomics data processing pipeline:

• Peak detection (XCMS)
• Alignment and grouping
• Metabolite identification (HMDB, MassBank)
• Statistical analysis

List Available Skills

bc7 skill list

Skill Parameters

Each skill accepts common parameters:

Creating Custom Skills

Create a skill definition in YAML:

name: my-custom-skill
description: Custom analysis workflow
steps:
  - name: qc
    tool: fastqc
    operation: quality_control
  - name: align
    tool: star
    operation: alignment
    depends_on: [qc]
  - name: count
    tool: featurecounts
    operation: quantification
    depends_on: [align]

Register the skill:

bc7 skill register ./my-skill.yaml