nextflow_config

PipelineLint.nextflow_config() → Dict[str, List[str]]

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.

Note

These config variables must be set in nextflow.config or another config file imported from there. Any variables set in nextflow script files (eg. main.nf) are not checked and will be assumed to be missing.

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 pipelines 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

  • params.custom_config_version

    • Should always be set to default value master

  • params.custom_config_base

    • Should always be set to default value:

    https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}

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)

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

  • params.max_cpus: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow

    `

    resourceLimits`directive in config files.

  • params.max_memory: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow

    `

    resourceLimits`directive.

  • params.max_time: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow

    `

    resourceLimits`directive.

    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'.
Note

You can choose to ignore tests for the presence or absence of specific config variables by creating a file called .nf-core.yml in the root of your pipeline and creating a list the config variables that should be ignored. For example:

lint:
  nextflow_config:
    - params.input

The other checks in this test (depreciated syntax etc) can not be individually identified, but you can skip the entire test block if you wish:

lint:
  nextflow_config: False

The configuration should contain the following or the test will fail:

  • A test configuration profile should exist.

The default values in “nextflow.config“ should match the default values defined in the “nextflow_schema.json“.

Note

You can choose to ignore tests for the default value of an specific parameter by creating a file called .nf-core.yml in the root of your pipeline and creating a list the config parameters that should be ignored. For example to ignore the default value for the input parameter:

lint:
  nextflow_config:
    - config_defaults:
        - params.input