update default nextclade dataset tag to "2023-09-21T12:00:00Z" for all TheiaCov wfs #208
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…". applied on wfs theiacov clearlabs, fasta, ilmn pe, ilmn se, ont
* skeleton on kmerfinder task * remove kmerfinder_db_name * still trying to get kmerfinder to run * is this working now?!? * first working version of kmerfinder task * parse top hit * make results output file optional * final version of task (for now..) * add kmerfinder_bacteria to theiaprok! * fix typo * pass empty file for tests - kmerfinder_db * fix input json * add kmerfinder query coverage to theiaprok SE, PE, FASTA and ONT * remove undeeded skip on kmerfinder (set to false by default) * fix ops * update md5sum (part1) * update md5sum (part2) * fiz sister typo * missed a file * update CI * add kmerfinder_template_coverage to theiaprok output * expose database name on kmerfinder outputs * update md5sum * fix bug - headers being outputed to datatable
…". applied on wfs theiacov clearlabs, fasta, ilmn pe, ilmn se, ont
….com/theiagen/public_health_bioinformatics into cjk-nextclade-sc2-tag-update-default
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branch has been rebased, will update CI momentarily |
kapsakcj
changed the title
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Tests to run prior to marking ready for review. Will check the box when run successfully and outputs have been reviewed 👀
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sage-wright
previously approved these changes
Oct 12, 2023
kapsakcj
dismissed
sage-wright’s stale review
The merge-base changed after approval.
sage-wright
previously approved these changes
Oct 12, 2023
kapsakcj
dismissed
sage-wright’s stale review
The merge-base changed after approval.
|
? what is happening with these stale reviews. I didn't dismiss anything! I have never seen this before |
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Stop it Curtis!! Yeah, I'm not sure. I'll merge quickly next time haha |
sage-wright
previously approved these changes
Oct 12, 2023
kapsakcj
dismissed
sage-wright’s stale review
The merge-base changed after approval.
sage-wright
previously approved these changes
Oct 12, 2023
michellescribner
previously approved these changes
Oct 12, 2023
kevinlibuit
approved these changes
Oct 12, 2023
kevinlibuit
previously approved these changes
Oct 12, 2023
kapsakcj
dismissed stale reviews from kevinlibuit, michellescribner, and sage-wright
The merge-base changed after approval.
kevinlibuit
approved these changes
Oct 12, 2023
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applied on wfs: theiacov clearlabs, fasta, ilmn pe, ilmn se, ont
🛠️ Changes Being Made
Updates default
nextclade_dataset_tagfor sars-cov-2 to be up to date (as of 2023-10-10) across 5 TheiaCov workflows🧠 Context and Rationale
Staying up-to-date. Specific to sars-cov-2 (as is many of the default inputs for TheiaCov workflows)
📋 Workflow/Task Steps
Inputs
N/A
Outputs
N/A
🧪 Testing
Locally
Did not test locally, will test all workflows in Terra
Terra
🔬 Quality checks
Pull Request (PR) checklist: