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