workflows updated with newer tools, added missing

[astrovsky01]

No description provided.

[astrovsky01]

How do I lint a workflow? I took what came from downloading off of an instance.

[bgruening]

source /home/travis/miniconda3/bin/activate galaxy_training_material && \
	bash bin/validate-json.sh && \
	bash bin/validate-workflow-tags.sh

[bedroesb]

@astrovsky01 Since #1724 and #1715 it is mandatory for a workflow on GTN to have the correct tags and annotation. I will add this workflow linting to planemo hopefully this week. You could fix this travis error easily by editing the workflow file. Make sure following attributes are filled in like this:

"annotation": "Unicycler Assembly",
...
...
"tags": [	    
    "assembly"
  ]

and

"annotation": "De novo transcriptome reconstruction with RNA-Seq",
...
...
"tags": [
    "transcriptomics"	
  ],

in the other file

[astrovsky01]

@bedroesb thank you, I appreciate it!

[bedroesb]

@astrovsky01 no problem ! We hope that if these workflows are than added to an instance, people can find them back easier.

[almahmoud]

Probably not necessary, but I'd also suggest changing the names to remove the numbering we're using internally (i.e. WF2, WF4) and just match the tutorial name

[bgruening]

@astrovsky01 have you checked that those workflows also follow the training material? Do we need to adjust the hands-on material because of parameter changed etc...?

[astrovsky01]

@bgruening they don't change the training, except the ones I added to the PR. It's more about updating tools to most recent versions.

[astrovsky01]

@bgruening Does anything else need to be changed?

[bgruening]

Sorry for the delay, didn't get any notification for the last 2 weeks, trying to catch up.