Create a subworkflow

This command creates a new nf-core subworkflow from the nf-core subworkflow template. This ensures that your subworkflow follows the nf-core guidelines. The template contains extensive TODO messages to walk you through the changes you need to make to the template. See the subworkflow documentation for more details around creating a new subworkflow, including rules about nomenclature and a step-by-step guide.

You can create a new subworkflow using nf-core subworkflows create.

This command can be used both when writing a subworkflow for the shared nf-core/modules repository, and also when creating local subworkflows for a pipeline.

Which type of repository you are working in is detected by the repository_type flag in a .nf-core.yml file in the root directory, set to either pipeline or modules. The command will automatically look through parent directories for this file to set the root path, so that you can run the command in a subdirectory. It will start in the current working directory, or whatever is specified with --dir <directory>.

The nf-core subworkflows create command will prompt you with the relevant questions in order to create all of the necessary subworkflow files.

nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force