nextflow-io
- 22 skills
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- 6 hours ago last updated
- ▌ Sequence Report · nextflow-ioFormat a sequencing or genome-assembly summary as a standardized QC report. Use this skill whenever the user asks for a sequence, assembly, or read-QC summary or verdict.
- ▌ Metadata Ontology · nextflow-ioMap free-text sequencing-sample metadata to controlled-vocabulary ontology terms. Use this skill whenever labelling a sample's organism, tissue/cell type, disease, or assay from its metadata.
- ▌ Style · nextflow-ioHouse writing style for this module's reports. Use whenever writing any report text, note or summary.
- ▌ QA Report · nextflow-ioFormat an assembly QC report as the standardized MOD-QA block. Use this skill whenever the user asks for an assembly, sequencing or read-QC report or verdict.
- ▌ Run Module · nextflow-ioRun Nextflow Registry modules natively using `nextflow module` commands. Use when running, listing, or getting info about Nextflow modules.
- ▌ Create Workflow · nextflow-ioINVOKE THIS SKILL IMMEDIATELY when user asks to: write/create/build a Nextflow pipeline or workflow, create any bioinformatics pipeline (RNA-seq, DNA-seq, variant calling, ChIP-seq, etc.), or compose/chain Nextflow modules from the Nextflow Registry. This skill handles all Nextflow workflow creation tasks.
- ▌ Launch Workflow · nextflow-ioLaunch Nextflow pipeline executions on cloud and HPC clusters via Seqera 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 Seqera Platform.
- ▌ Install Nextflow · nextflow-ioInstall 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.
- ▌ Migrate Nextflow Code · nextflow-io bundleMigrate Nextflow pipeline code to newer language requirements. Use when fixing strict syntax errors, replacing versions channels with topic channels, migrating from `publishDir` to workflow outputs (the `output {}` block), or adding static typing (typed processes/workflows, records, typed params).
- ▌ Preview · nextflow-ioStart local MkDocs preview server to view training material changes. Use when editing documentation, checking formatting, or testing how content renders before committing.
- ▌ Validate Training Materials · nextflow-io bundleRun comprehensive validation and review checks including heading numbering, TODO/FIXME comments, Nextflow script conventions, orphaned files, admonition syntax, lesson structure, formatting, content accuracy, and teaching effectiveness. Use when validating, reviewing, or checking training materials quality, lesson quality, or before committing changes.
- ▌ Find Todo And Fixme Comments · nextflow-ioSearch markdown files, Nextflow scripts, and config files for TODO/FIXME comments, categorize by priority, and provide actionable recommendations. Use when you need to identify pending work or track technical debt.
- ▌ New Lesson · nextflow-ioCreate a new numbered lesson page within an existing training module. Use when adding a new topic like '05_error_handling.md' to an existing course.
- ▌ New Module · nextflow-ioScaffold a complete new training module with standard directory structure, index, orientation, lessons, survey, and next-steps files. Use when creating a new course like 'Advanced Pipelines' or a new domain module.
- ▌ Add Exercise · nextflow-ioAdd an interactive exercise with solution to an existing lesson. Creates properly formatted exercise and solution admonition blocks. Use when a lesson needs hands-on practice.
- ▌ Docker Environment Setup · nextflow-ioSet up a Docker container for running Nextflow training examples. Handles basic setup, Docker-outside-of-Docker (DooD) for containerized processes, ARM Mac platform emulation, and troubleshooting. Use when you need to run Nextflow examples in a consistent environment.
- ▌ Run Tutorial Walkthrough · nextflow-io bundleWalk through a training tutorial as a user would, progressively building examples exactly as instructed, running all commands, and verifying results against solutions. Use when testing tutorials end-to-end or validating that instructions are correct and complete.
- ▌ Stop Preview · nextflow-ioStop a running MkDocs preview server. Use when port 8000 is busy, switching tasks, or done editing documentation.
- ▌ Test Nextflow Example Script · nextflow-ioTest a Nextflow script by running it, verifying outputs, testing resume functionality, and comparing results with documentation. Use when validating that example scripts work correctly and match their documentation.
- ▌ Check Code Block Highlights · nextflow-ioVerify that hl_lines attributes in markdown code blocks correctly highlight the intended lines. Use when reviewing documentation with code examples, especially Before/After comparisons, or when highlights seem incorrect.
- ▌ Check Inline Code Formatting · nextflow-ioReview inline code in markdown files for proper formatting and syntax highlighting. Check for missing backticks on CLI flags, filenames, and code elements. Verify that inline syntax highlighting (#!groovy) is used appropriately. Use when reviewing documentation or quiz questions.
- ▌ Summit Cms · nextflow-ioEdit Nextflow Summit website content in Sanity and publish it to the live site. Use whenever a task involves changing CMS content for the summit-website repo — talks/events, speakers, posters, sponsors, agenda, page copy, embedding YouTube recordings — or making such changes appear on summit.nextflow.io (which needs a Netlify rebuild). Covers the no-deployed-schema write workaround and the master-branch deploy gotcha.