nextflow_config

PipelineLint.nextflow_config()

Checks the pipeline configuration for required variables.

All nf-core pipelines are required to be configured with a minimal set of variable names. This test fails or throws warnings if required variables are not set.

The following variables fail the test if missing:

• params.outdir: A directory in which all pipeline results should be saved
• manifest.name: The pipeline name. Should begin with nf-core/
• manifest.description: A description of the pipeline
• manifest.version
  • The version of this pipeline. This should correspond to a GitHub release.
  • If --release is set when running nf-core lint, the version number must not contain the string dev
  • If --release is _not_ set, the version should end in dev (warning triggered if not)
• manifest.nextflowVersion
  • The minimum version of Nextflow required to run the pipeline.
  • Should be >= or !>= and a version number, eg. manifest.nextflowVersion = '>=0.31.0' (see Nextflow documentation)
  • >= warns about old versions but tries to run anyway, !>= fails for old versions. Only use the latter if you know that the pipeline will certainly fail before this version.
  • This should correspond to the NXF_VER version tested by GitHub Actions.
• manifest.homePage
  • The homepage for the pipeline. Should be the nf-core GitHub repository URL, so beginning with https://github.com/nf-core/
• timeline.enabled, trace.enabled, report.enabled, dag.enabled
  • The nextflow timeline, trace, report and DAG should be enabled by default (set to true)
• process.cpus, process.memory, process.time
  • Default CPUs, memory and time limits for tasks
• params.input
  • Input parameter to specify input data, specify this to avoid a warning
  • Typical usage:
    • params.input: Input data that is not NGS sequencing data

The following variables throw warnings if missing:

• manifest.mainScript: The filename of the main pipeline script (should be main.nf)
• timeline.file, trace.file, report.file, dag.file
  • Default filenames for the timeline, trace and report
  • The DAG file path should end with .svg (If Graphviz is not installed, Nextflow will generate a .dot file instead)
• process.container
  • Docker Hub handle for a single default container for use by all processes.
  • Must specify a tag that matches the pipeline version number if set.
  • If the pipeline version number contains the string dev, the DockerHub tag must be :dev

The following variables are depreciated and fail the test if they are still present:

• params.version: The old method for specifying the pipeline version. Replaced by manifest.version
• params.nf_required_version: The old method for specifying the minimum Nextflow version. Replaced by manifest.nextflowVersion
• params.container: The old method for specifying the dockerhub container address. Replaced by process.container
• igenomesIgnore: Changed to igenomes_ignore

  Note

  The snake_case convention should now be used when defining pipeline parameters

The following Nextflow syntax is depreciated and fails the test if present:

• Process-level configuration syntax still using the old Nextflow syntax, for example: process.$fastqc instead of process withName:'fastqc'.