nextflow

Plugin nextflow from marketplace nextflow-plugin in seqeralabs/nextflow-plugin. Commands read from the repo's manifest — 6 days ago.

Skills (28)

• audit-conversion-readiness

  Read-only first-pass audit of source material (scripts, notebooks, Snakemake/WDL/CWL workflows, legacy in-house pipelines) before converting or migrating it to Nextflow. Inventories every hardcoded or external file path, probes which of them are actually reachable from this session, and flags tool c

• build-nextflow-pipeline

  Plan and scaffold a new Nextflow DSL2 pipeline from source material — scripts, repositories, Jupyter/R notebooks, papers, or informal instructions. Drives the planning phases before any .nf code is written: mapping the data flow, critiquing it, shaping channels and metadata, scoping subworkflows, hu

• ce-credentials-setup

  Set up Nextflow Platform compute environments (Seqera Compute, AWS Batch, Kubernetes) and the cloud or cluster credentials they need. Walks through gathering prerequisites — IAM keys, bearer tokens, certificates, regions, work directories — and then calling platform_create_credentials and platform_c

• create-container

  Build, claim, or recommend a verified container for a bioinformatics tool — and prove it runs the intended command on representative test data before handing it off for module authoring. Make sure to use this skill whenever the user wants to containerize a tool, wrap a tool for a Nextflow module, se

• debug-local-run

  Debug a local Nextflow pipeline run. Analyzes .nextflow.log, work directories, and task error logs to identify failures and suggest fixes. Use when user asks to debug their last run, diagnose pipeline errors, or understand why a run failed.

• debug-seqera-failed-run

  Debug failed Nextflow Platform pipeline runs. Fetches workflow details, failed tasks, and logs to identify root causes and suggest fixes. Use when the user asks why a Platform run failed, to debug the last run, to diagnose a Seqera workflow error, or to triage recurring failures across runs and prop

• find-alternative-tools

  Given a named bioinformatics analysis step (e.g. "multiple sequence alignment", "somatic variant calling", "protein structure prediction", "single-cell demultiplexing"), find the credible alternative tools that could implement it, with pros/cons, license notes, typical compute requirements, maintena

• install-nextflow

  Install or upgrade Nextflow on the user's machine. Use when the user wants to install Nextflow, check their current Nextflow version, upgrade Nextflow, or set up the prerequisites (Java 17+) needed to run Nextflow.

• launch-workflow

  Launch Nextflow pipeline executions on cloud and HPC clusters via Nextflow Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Nextflow Platform.

• maintain-nf-core-pipeline

  Maintain an existing nf-core pipeline: work on the `dev` branch, resolve outstanding template-sync PRs, update shared modules from upstream, then patch any remaining code. Use whenever the user asks to update, maintain, sync, modernize, or contribute to an nf-core pipeline; whenever they mention res

• migrate-from-snakemake

  Convert Snakemake workflows to idiomatic Nextflow DSL2 pipelines with a test-first, modular migration loop. Trigger: "snakemake to nextflow", "migrate from snakemake", "convert snakefile", "/migrate-from-snakemake".

• migrate-nextflow-code

  Migrate a Nextflow pipeline to new language patterns.

• nextflow-config

  Generate and explain Nextflow configuration files. Use when user asks to create, modify, debug, or understand nextflow.config files. Covers all config scopes, process selectors, profiles, executor settings, and container runtimes.

• nextflow-development

  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 r

• nextflow-history

  Analyze local Nextflow run history and cache. Use when user asks about their recent local runs, wants to see what pipelines they've executed, understand run lineage, inspect the Nextflow cache, or correlate runs with work directories. Uses run history, task cache metadata, and Nextflow logs supplied

• nextflow-output-patterns

  Use this skill when writing or reviewing any Nextflow workflow that aggregates per-sample outputs into a combined file, joins channels with a remainder mode, or groups tuples for per-group processing. Covers the operator idioms — `collectFile`, `join`, `groupTuple`, channel-level null handling — tha

• nextflow-schema

  Generate canonical nextflow_schema.json, optional nextflow_schema.minimal.json, and sample sheet schema files for Nextflow pipelines. Use when user asks to create, update, or validate a pipeline parameter schema or sample sheet schema. Covers type inference, parameter grouping, nf-core conventions,

• nf-data-lineage

  Explore Nextflow data lineage to trace where outputs came from and what inputs produced them. Uses the configured lineage store and `nextflow lineage` CLI. Requires Nextflow 25.04+ with lineage.enabled=true. Use when the user asks about provenance, data origins, reproducibility, or output traceabili

• nf-docker-scripts

  Guide users on how to manage scripts in Nextflow processes and Docker images. Covers shared helper commands, template directive, inline scripts, and why module binaries should not be recommended by default. Use when the user asks about Docker images for Nextflow, where to put scripts, how to handle

• nf-pipeline-design

  Make sure to use this skill whenever you are designing, writing, reviewing, or refactoring a Nextflow DSL2 pipeline with a focus on STRUCTURE — the shape of `main.nf`, where subworkflows belong, when something is a module vs. an operator, how channels and metadata flow. Trigger phrases include "desi

• nf-plugin-development

  Create Nextflow plugins using the official nf-plugin-template and publish to the Nextflow plugin registry. Covers extension points (operators, functions, factories, executors, trace observers), project structure, testing, and publishing. Use when the user wants to create a new plugin or add custom f

• nf-plugin-legacy-migration

  Migrate legacy Nextflow plugins to the new plugin registry format. Covers converting plugins that use the old GitHub-based nf-plugins-index to the modern registry.nextflow.io approach. Use when the user has an existing plugin using the legacy format or wants to understand the differences between old

• nf-test

  Testing Nextflow pipelines with nf-test. Use when setting up nf-test, writing pipeline tests, testing modules/subworkflows, using nft-utils assertions, or debugging test failures. Trigger phrases include "test nextflow", "nf-test", "test pipeline", "write test for workflow", "snapshot testing".

• repair-workflow

  Repair or debug an existing Nextflow workflow or pipeline. Use when the user asks to fix, debug, or improve an existing workflow, especially when choosing the right validation loop matters more than writing new workflow structure. Also use for pipeline lint, config validation and preview/compilation

• run-module

  Run Nextflow Registry modules natively using `nextflow module` commands. Use when running, listing, or getting info about Nextflow modules, including process modules (a single tool) and workflow modules (subworkflows that chain several modules).

• search-existing-modules

  Given a bioinformatics tool name (e.g. MAFFT, Boltz, bcftools, salmon), search for existing Nextflow module implementations in priority order — nf-core/modules first, then a supplied source repository, then the broader community (GitHub, nf-core pipelines, biorxiv/arxiv supplementary pipelines). Ret

• seqera-data-links

  Add, list, inspect, browse, update, and delete data links in Nextflow Platform workspaces. Use when asked to connect S3/GCS/Azure storage, manage Data Explorer entries, create data links, or troubleshoot bucket validation and storage access.

• seqerakit

  Write seqerakit YAML configuration files for automating Nextflow Platform setup. Covers pipelines, launch, compute-envs, datasets, credentials, and other entity types. Trigger: "seqerakit", "seqerakit YAML", "write seqerakit config", "automate platform setup", "tw YAML", "infrastructure as code for

MCP servers (1)

• seqera

  connects to: https://mcp.seqera.io/mcp

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