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theiagen / public_health_bacterial_genomics

GNU Affero General Public License v3.0
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Fja tbprofiler update #174

Closed frankambrosio3 closed 1 year ago

frankambrosio3 commented 1 year ago

just updated to the later tbprofiler docker image tag and swapped quay for staphb

kapsakcj commented 1 year ago

Looks like the WDL task will need to be updated. Found this in the log files when using this dev branch:

usage: tb-profiler
{profile,vcf_profile,fasta_profile,lineage,spoligotype,collate,reprofile,reformat,create_db,update_tbdb,batch,list_db,version}
...
tb-profiler: error: unrecognized arguments: --version

I think tbprofiler still ran as expected and produced the outputs but the version is an empty string.

I'll push a commit to fix when I get a chance

kapsakcj commented 1 year ago

After adjusting the WDL code for the version capture, everything ran as expected in Terra. Correctly captured the version info as well as the other tbprofiler expected outputs ✔️

This branch is quite far behind main branch (174 commits behind) but seeing as this is only a minor task edit, I don't think it will matter.

You could pull in the latest changes from main into this branch and re-run tests just to ensure latest changes to TheiaProk wfs do not interfere with these changes

kapsakcj commented 1 year ago

Tested successfully in Terra after bringing this dev branch up to date with main, so I'm going to go ahead and merge the PR