pvanheus

Question: `output_options` are meant to be exclusive. When I create an input object like: ``` yaml sequences: class: File path: /home/pvh/Data/fasta/full_msa.fasta format: edam:format_1929 output_options: output_fasta: true output_phylip: true $namespaces: edam:...

@fjrmoreews is this PR still relevant? I tried the two tools that are currently in bio-cwl-tools and got usable outputs.

To clarify, when using the existing tools, if the following workflow is given an input file like: ``` genome: class: File format: edam:format_1929 path: /home/pvh/Data/fasta/MN908947_3_Wuhan-Hu-1.fasta reads: - class: File format:...

Note that even the updated version of the tools triggers a warning as cwltool interprets the Javascript expression literally. The updated tools do, however, work: ``` $ cwltool --debug workflow.cwl...

Another update - the latest version does not use InlineJavascript for anything and does not provoke any warnings when run in a workflow.

One more update: change to recommended snake_case for input and output names and kebab-case for tool names. Also make `index_name` parameter for `bwa-index.cwl` optional. Honestly I do not like how...

@mb1069 - can you review this PR please?

@xinhuang66 is there any particular functionality you want to BBtools? This could help focus work on a wrapper.

Both the Augustus and Augustus Train wrappers using `tar` with the `-z` option which is not supported in all versions of tar (e.g. the one in BusyBox doesn't support it)....

See issue on the Ansible repo: https://github.com/BaobabLims/baobab-ansible/issues/3