bio-workflow-management-nextflow-pipelines
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on cloud platforms (AWS, Google Cloud), or leveraging nf-core community pipelines.
npx skills add BioTender-max/awesome-bio-agent-skills --skill nextflow-pipelines --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: FastQC 0.12+, MultiQC 1.21+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, fastp 0.23+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Nextflow Pipelines **"Create a scalable containerized pipeline with Nextflow"** → Build DSL2 workflows with process definitions, channel-based data flow, Docker/Singularity container support, and cloud execution (AWS, Google Cloud) for portable bioinformatics analysis. - CLI: `nextflow run main.nf` for pipeline execution - Groovy: DSL2 process/workflow syntax for pipeline definition ## Basic Pipeline Structure ```groovy // main.nf nextflow.enable.dsl=2 params.reads = "data/*_{1,2}.fq.gz" params.outdir = "results" process FASTQC { input: tuple val(sample_id), path(reads) output: path("*.html"), emit: html path("*.zip"), emit: zip script: """ fastqc ${reads} """ } workflow { Channel.fromFilePairs(params.reads) | FASTQC } ``` ## DSL2 Modules
- Version Compatibility
- Basic Pipeline Structure
- DSL2 Modules
- Config File
- Container Support
- Channel Operations
- Subworkflows
- Cluster Execution
- AWS/Cloud Execution
- Resource Labels
- Error Handling
- Caching and Resume
- Complete RNA-seq Pipeline
- Related Skills
Run on AWS nextflow run main.nf -profile awsbatch -bucket-dir s3://my-bucket/work Resume from last run nextflow run main.nf -resume Clean work directory nextflow clean -f Show execution trace nextflow log
What does the bio-workflow-management-nextflow-pipelines skill do?
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on cloud platforms (AWS, Google Cloud), or leveraging nf-core community pipelines.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill nextflow-pipelines --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.