Research & Science · Nextflow

Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/.

bactopia/bactopia

Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia…

bactopia/bactopia

Cut a new tagged release of the dockstore/dockstore webservice (alpha/beta/rc/stable/hotfix), following the dockstore-deploy wiki's Hubflow + Maven CI-friendly-versions process.

dockstore/dockstore

Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas.

bactopia/bactopia

Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.

davila7/claude-code-templates

Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate.

bactopia/bactopia

Latch platform for bioinformatics workflows. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Review staleness of reference docs under .agents/docs/ using bactopia-docs --validate.

bactopia/bactopia

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.

BioTender-max/awesome-bio-agent-skills

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP.

K-Dense-AI/scientific-agent-skills

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs.

K-Dense-AI/scientific-agent-skills

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow.

K-Dense-AI/scientific-agent-skills

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows.

K-Dense-AI/scientific-agent-skills

Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.

ClawBio/ClawBio

Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.

ClawBio/ClawBio

Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on…

GPTomics/bioSkills

Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed.

GPTomics/bioSkills

Runs and configures curated nf-core community Nextflow pipelines (rnaseq, sarek, atacseq, methylseq, ampliseq, taxprofiler, fetchngs) reproducibly, pinning the pipeline revision with -r and…

GPTomics/bioSkills

Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry…

GPTomics/bioSkills

Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO…

GPTomics/bioSkills

Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.

ClawBio/ClawBio

Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

This skill is applicable when using LaminDB. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Workflows for RNA-seq, GWAS, and variant calling in genomic research

wentorai/research-plugins

CD-GPT 生成式生物基础大模型，对 DNA/RNA/蛋白质序列预训练，支持单分子与多分子联合分析的预测与生成. An agent skill from infometa/workbuddyskills.

infometa/workbuddyskills