Come up with a standard & documentation on subworkflows

[FriederikeHanssen]

TODO:

Issues:

• Installing subworkflows with tools: Get a list of modules that need to be installed (how to find them) -> tools needs to install missing modules in pipeline/repo -> install subworkflow (tools command needed, probably once the new people join Seqera/QBiC (next few months))
• Testing subworkflows
• [ ] https://github.com/nf-core/modules/issues/2218

[edmundmiller]

Notes from yesterday (per @lescai):

• input file format
  • Most frequent input format(s) is/are included (if several, alphabetical order) (updated at 5:30)
  • make sure it is in yml tags, i.e. can be search on website
  • subworkflow should support all possible file types supported by the tool
  • review to make sure same input format is chosen across subworkflows for consistency
• operation(s): no specific ordering guideline
  • The operation should describe as best as possible the sub-workflow task
  • Need to come up with an onthology for similar operation with different names i.e. 'align' for 'Mapping' and 'alignemnt'
• tool name(s): alphabetical ordering, each tools once
  • tool name (i.e. samtools) and not function (i.e. samtools sort) is used
  • If several tools are used in the subworkflow, the tool name(s) should be ordered as used in the subworkflow and separated by underscores
  • review to pick up potential issues with identical names referring to different tool functions used

• All lower case