Add 'Quality and Contamination control' workflow

clsiguret commented 5 months ago

This workflow comes from the ABRomics project and can be used for any bacterial genomic analysis: Quality and Contamination control for paired end data

This workflow uses 3 databases which must be available on http://datacache.galaxyproject.org/:

kraken2_database (Kraken2): k2_minusb_20210517
bracken_database (Bracken): k2_minusb_20210517
ncbi_taxonomy (Recentrifuge): 2022-03-08

We followed the recommendation to publish the workflow (licence, author list and email, steps annotations...)

[x] Workflow imported from usegalaxy.fr using planemo workflow_test_init to use a valid invocation
[x] Workflow tests passed using planemo test command on the usegalaxy.eu server
[x] Readme.md written
[x] CHANGELOG.md written
[x] .dockstore.yml written

bebatut commented 4 months ago

We need this PR to be merged as soon as possible to have time to update our workflows and tutorials before GCC and the French Bioinformatics conference next week. If I do not get any "No do not merge" by the middle of the day, I will merge it and we will make a V2 of the workflow later.

clsiguret commented 4 months ago

Again, very nice work, thanks a lot!

Thanks you (@mvdbeek) and @wm75 :smile: and @bebatut :wink:

mvdbeek commented 4 months ago

Attention: deployment failure!

https://github.com/galaxyproject/iwc/actions/runs/9544770124

clsiguret commented 4 months ago

Attention: deployment failure!

https://github.com/galaxyproject/iwc/actions/runs/9544770124

the problem comes from workflows/bacterial_genomics/bacterial_genome_assembly ?

mvdbeek commented 4 months ago

No, the version in the .dockstore.yml field is the version of the .dockstore.yml schema, it should be 1.2 always, I've fixed that in https://github.com/galaxyproject/iwc/commit/9458220b6fd44bb797a645877676cdd9ba7f2233

galaxyproject / iwc

Add 'Quality and Contamination control' workflow #437