workflow parameters description

[ChristopherBarrington]

these parameters could be clearer. they are meant to be a list of keys that are used in the workflow that will be taken from the parameters object.

[ChristopherBarrington]

1. user configurable parameters to list the key from parameters file. need to think about default/guessed values
2. internal parameters that cannot be accessed from user

25

[ChristopherBarrington]

• have a usage/parameters guide that lists all user parameters, taken from a yaml.
• add a user parameters section to workflow docs that will add a badge for each workflow to each parameter
• use the user/default/process nomenclature still

[ChristopherBarrington]

split usage guides into

1. Quickstart
2. more detail
3. parameters

[ChristopherBarrington]

need to parse params file and add in defaults for missing (required) parameters

defaults

• [ ] fastq paths: /camp/stp/sequencing/inputs/instruments/data/lab/scientist/lims/data/*

checks

• [ ] paths and files exist
• [ ] feature type has expected number of libraries
• [ ] make sure that the assay types part are not empty