36 skills · sorted by relevance
Build, run, and troubleshoot data processing pipelines with Nextflow and nf-core. The skill guides modular workflow development, input preparation, testing, cached restarts, and configuration for local computers, computing clusters, or cloud environments.
Build and operate bioinformatics workflows on Latch using Python, Nextflow, or Snakemake. Configure computing resources and input forms, move data, connect Registry records, and register, debug, launch, and monitor analysis runs.
Build and operate genomics workloads on DNAnexus using its command-line tools and Python SDK. The skill covers data transfers, app configuration checks, workflow imports, execution monitoring, and explicit cost controls for reproducible analysis workflows.
Prepare and launch nf-core/pacsomatic workflows for matched tumor and normal PacBio HiFi samples. Generate sample sheets and launch files from unaligned BAM inputs, run local checks, submit cluster launchers, and troubleshoot startup failures.
Run nf-core workflows on local sequencing files or public GEO/SRA datasets to analyze gene expression, genetic variants, or chromatin accessibility. The skill guides environment checks, sample table preparation, workflow configuration, execution, and output verification.
Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. Use when deciding channel/dataflow (Nextflow) vs rule-based (Snakemake) authoring; wiring queue vs value channels and fixing shared-reference exhaustion with .first(); composing DSL2 modules and subworkflows with take/main/emit; selecting container/conda profiles and pinning images by digest for portability across local/SLURM/LSF/AWS Batch/Google Batch/Kubernetes executors; diagnosing why -resume misses the cache (nondeterministic input order, mtime on network filesystems, mutable :latest tags) with cache 'lenient' and -dump-hashes; managing work/ vs publishDir and dynamic retry escalation; and choosing whether to adopt an nf-core community pipeline or author from scratch.
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Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
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Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.
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Access ENCODE uniform analysis pipelines, generate user-specific Nextflow/WDL pipelines, manage compute resources, and integrate with cloud platforms. Use when the user wants to understand ENCODE pipelines, run pipelines on their own data, generate custom Nextflow workflows from ENCODE pipeline code, check compute requirements (CPU/GPU/memory), run pipelines in background, or integrate with Google Cloud, AWS, or other cloud platforms. Also use when the user asks about ENCODE pipeline outputs, processing standards, software versions, or wants to replicate ENCODE processing. Covers local execution, HPC, and cloud deployment with resource-aware scheduling. Use this skill for ANY pipeline execution, workflow generation, or compute resource management task involving ENCODE data.
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Prepare bulk RNA-seq sequencing files or quantification outputs for gene-level comparisons. Check sample information and data quality, configure processing workflows, and assemble validated count tables and metadata for downstream differential expression analysis with PyDESeq2.
Get oriented with a biological research plugin by checking connected research tools and reviewing available analysis skills. Receive a connection summary, optional setup guidance, and suggested starting points for literature searches, sequencing analysis, drug discovery, or research planning.
Prepare single-cell or single-nucleus RNA-seq analysis by checking inputs and selecting workflows that turn FASTQ sequencing files into count matrices. Route quality checks, cell annotation, clustering, and UMAP visualization to the embedded downstream skill.
Organize ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag inputs and route them to suitable analysis workflows. Covers initial quality checks and preparation for finding peaks, genomic regions with concentrated signal, and comparing them across samples.
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
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Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
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Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs, or comparing CPU and GPU workflow outputs. Adds optional GPU steps in-place with runtime toggles (default off). Do NOT use for individual pbrun command routing — use parabricks.
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This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakes, or ensuring data lineage and reproducibility in biological research. It covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integration with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
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Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
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Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets. Integrates with Nextflow, Snakemake, W&B, scVI. For scRNA-seq use scanpy; for ontology lookups use bionty.
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Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.
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Use ClawBio for local-first bioinformatics agent workflows: install and run its skill library, route genomic or omics inputs, create reproducible reports, connect optional MCP or Nextflow integrations, and author or validate skills.
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Think and work like an expert Computational Scientist. Use when a task calls for Computational Scientist judgment. Reasons from Roache code/solution verification and ASME V&V 10/20/40 credibility through MMS/GCI, UQ ensembles, and Snakemake/Nextflow/CWL pipelines with conda-lock/Apptainer provenance while treating environment drift, workflow cache staleness, and validation-vs-calibration conflation as first-class failure modes.
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Think and work like an expert Bioinformatics Engineer. Use when a task calls for Bioinformatics Engineer judgment. Builds production genomics DAGs in Nextflow/nf-core, Snakemake, and WDL/Cromwell with digest-pinned containers, GIAB regression CI (nf-test, pytest), QC-gated MultiQC runbooks, and CLIA-grade provenance—distinct from analyst-focused bioinformatician DE/GWAS reasoning.
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Patterns for building, maintaining, and scaling bioinformatics workflows. Covers Nextflow, Snakemake, WDL/Cromwell, container orchestration, and best practices for reproducible computational biology. Use when ", " mentioned.
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