Azurized wdls #1239
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Azurized wdls #1239
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* add logic to choose which docker * fix param_meta and import * add cloud provider to checkinput * handle hard coded white list paths in CheckInputs.wdl * last few dockers * last few dockers * last few dockers * change error msg * use ubuntu image * use ubuntu image * change whitelists * point to azure public whitelists * add sas token * echo whitelist * echo whitelist * testing for coa * testing for coa * change back to terra buckets for whitelists * change whitelists to point at public azure bucket * files to strings * print statemtns to checkinputs * string to files * change to terra bucket paths * strings not files * append sas token * append sas token * append sas and use strings * back to bucket urls * back to bucket urls * use google cloud urls * using public urls * trying to export sas_token * trying to export sas_token * trying to export sas_token * terra on gcp * update azure whitelist files * changelogs * changelogs * changelogs * changelogs * fix some inputs * fix some inputs * fix some inputs * fix some inputs * update optimus dockers * warp_tools_docker_path for staralign * stop using ice lake as default * update pipeline docs * 2 threads * counting mode * changelogs --------- Co-authored-by: phendriksen100 <[email protected]> Co-authored-by: kayleemathews <[email protected]>
* ph logic to pass in docker images based on cloud provider * determine which whitelist files to use * update tests * add parameter metadata * add error handling in atac * fix comment * PR comments * update image and add utils * add import --------- Co-authored-by: phendriksen100 <[email protected]>
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optimus plumbing is failing with nondeterminism in empty drops. when using the emptyDrops comparison notebook (https://app.terra.bio/#workspaces/warp-pipelines/Multiome-test-workspace/analysis/launch/emptydrops_comparison.ipynb) the spearmen correlation between test/truth h5ad files was .99 scipy.stats.spearmanr(df.emptydrops_PValue_truth, df.emptydrops_PValue, axis=0, nan_policy='omit') |
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I think there are probably some additional documentation updates that need to be made here. I can probably take a look either this afternoon or tomorrow morning. |
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Co-authored-by: ekiernan <[email protected]>
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ekiernan
reviewed
Jul 15, 2024
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nikellepetrillo
commented
Jul 15, 2024
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kevinpalis
approved these changes
Jul 15, 2024
ekiernan
approved these changes
Jul 15, 2024
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Description
Summary of changes:
Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.