Snakemake standardized usage

[uniqueg]

Problem

V-pipe is listed in the Snakemake Workflow Catalog. However, it does not adhere to the standardized usage and therefore isn't listed in the default view (tab "Standardized usage") and can only be found after manually changing to a different view (tab "All workflows").

Adhering to the recommended standardized usage might increase the exposure of V-pipe, particularly, as the workflow -with the current number of stars- would be featured on the front page.

Solution

As described here, being listed in the "Standardized usage" section requires:

• the main workflow definition in file workflow/Snakefile
• workflow configuration instructions to be provided in config/README.md
• a .snakemake-workflow-catalog.yml file to configure usage instructions

As the first two conditions are already fulfilled, it appears that only the last condition needs to be addressed for V-pipe to be listed in the "Standardized usage" section.

Additional context

The allowed/required sections for the usage instructions configuration file (in YAML format) are described below:

usage:
  mandatory-flags: # optional definition of additional flags
    desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
    flags: # put your flags here
  software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
    conda: true # whether pipeline works with --use-conda
    singularity: true # whether pipeline works with --use-singularity
    singularity+conda: true # whether pipeline works with --use-singularity --use-conda
  report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations

A working example for a Snakemake Workflow Catalog configuration can be found, e.g., here for the ZARP workflow.