Lk add exome testing #1461
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Lk add exome testing #1461
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* add beta test optimus.yml * add beta test optimus.yml * add beta test optimus.yml
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ekiernan
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ekiernan
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Feb 18, 2025
* return method_config_name * return method_config_name * return method_config_name * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * cat github env * clean up * clean up * more clean up * more clean up * more clean up * more clean up * more clean up * more clean up * more clean up * more clean up * more clean up * trying to port optimus for fun!! * trying to port optimus for fun!! * trying to port optimus for fun!! * trying to port optimus for fun!! * update UpdateTestInputs.py to handle array inputs * update UpdateTestInputs.py to handle array inputs * update UpdateTestInputs.py to handle array inputs * fix branch name * fix branch name * fix branch name * fix branch name * fix branch name * try updating test inputs again * try updating test inputs again * try updating test inputs again * try updating test inputs again * try updating test inputs again * try updating test inputs again * fix setting the test type * fix setting the test type * fix setting the test type * fix setting the test type * fix setting the test type * fix setting the test type * fix the quote values function * fix the quote values function * fix the quote values function * fix the quote values function * pushing a commit to trigger * udate quote values to handle arrays? * udate quote values to handle arrays? * make truth path and results path dynamic * make pipeline_dir dynamic * fix submission url * fix submission url * make both tests the same * make both tests the same * add testsnm3c to dockstore yml * port snm3c * port snm3c * debugging fetch_dockstore_commit.py * debugging fetch_dockstore_commit.py * debugging fetch_dockstore_commit.py * debugging fetch_dockstore_commit.py * remove nested inputs * remove nested inputs * Lk atac test porting (#1457) Added changes for paired-tag tests * try to add testmultiome * add variant call test * additional changes to add variant calling test * add http imports to TestMultiome.wdl and Multiome.wdl * add TestReblockGVCF.wdl to the new testing framework * try to handle stucts * try to handle stucts * try to handle stucts * try to handle stucts * try to handle stucts * try to handle stucts * try to handle stucts * handle nested inputs * handle nested inputs * add wgs germline ss * try testing with removing always * Lk add exome testing (#1461) Added GHA testing for ExomeSingleSample * try testing with removing always * Rc test smartseq 3 (#1466) * smartseq action branch * remove old smartseq2 single nucleus path * gha test ss2sn * change DOCKSTORE_PIPELINE_NAME * update smartseq paths * fix destination cloud path * update the Dockstore pipeline name * readd smartseq2singlenucleus * try testing with removing always * add OVERALL_SUCCESS to all tests * Lk rnawithumis testing (#1467) Added GHA testing for RNAWithUMIsPipeline * add OVERALL_SUCCESS to all tests again * add OVERALL_SUCCESS to all tests again * add joint genotyping * add UltimaGenomicsWholeGenomeGermline * remove https and move generate file summary after all procesing is complete * fix summary tables for all ymls * update run_pipeline * update run_pipeline * update run_pipeline * update run_pipeline * update run_pipeline * Ultima Whole Genome Cram Only testing (#1472) Added Ultima Cram Only * try updating usercomment * try updating usercomment * try updating usercomment * try updating usercomment * try updating usercomment * try updating usercomment * move submission data file * move submission data file * move eof * move eof * move eof * move eof * move eof * move eof * move eof * move eof * input_file instead of test_input_file * input_file instead of test_input_file * input_file instead of test_input_file * input_file instead of test_input_file * add input json name to user comment * Updated pipeline_versions.txt with all pipeline version information * add ultima joint genotyping * add cram to unmapped bams * add exomereprocessing * add wholeGenomeReprocessing * remove truth_branch and replace with master * test out adding authorized_users.yml * test out adding authorized_users.yml * test out adding authorized_users.yml * test out adding authorized_users.yml * update post * update post * update post * update post * echo reponse * use np_jw_test_illumina_genotyping_arrays * use np_jw_test_illumina_genotyping_arrays * make testType not required * make testType not required * make testType not required * make testType not required * make testType not required * make testType not required * make testType not required * make testType not required * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * restructure how we check authed users * test out cram to ubam * dont convert float to scientific notation * Rc test slideseq 3 (#1475) * add testslideseq to dockstore * fix slideseq test wdl path * start slideseq yml with task wdls * update test wdl and yaml * fix testslideseq paths * Updated pipeline_versions.txt with all pipeline version information * update jobs to TestSlideSeq --------- Co-authored-by: GitHub Action <[email protected]> Co-authored-by: Nikelle Petrillo <[email protected]> * For workflow_dispatch, default based on target branch * For workflow_dispatch, default based on target branch * new way of chekcing auth * new way of chekcing auth * new way of chekcing auth * new way of chekcing auth * new way of chekcing auth * new way of chekcing auth * new way of chekcing auth * kick off tests * make terra failure message more visible * Updated pipeline_versions.txt with all pipeline version information * Updated pipeline_versions.txt with all pipeline version information * add new line * remove new line * Updated pipeline_versions.txt with all pipeline version information * remove new line * Updated pipeline_versions.txt with all pipeline version information * fix error message * disable auth check * Updated pipeline_versions.txt with all pipeline version information * remove whitelist auth check * add multiome * add multiome * add dockstore retry mechanism * Np abort jobs from previous commits (#1498) * add abort jobs functionality * add abort jobs functionality * add abort jobs functionality * add abort GHA functionality * add abort GHA functionality * add abort GHA functionality * add abort GHA functionality * add abort GHA functionality * add abort GHA functionality * try to add in test type to method config name * dont default to plumbing * dont default to plumbing * try to add test type to upload_test_inputs * try to add test type to upload_test_inputs * only abort plumbing jobs * only abort plumbing jobs * debugging * add test type to cancel terra runs * add test type to cancel terra runs * logigng info * logigng info * remove print * revert * revert firecloud_api.py * logging info method config name * logging info method config name * add testtpye to cancel and upload * quotes * quotes * bug after else * only abort plumbing gha jobs * install deps * move setup python * uncomment method config name filter * uncomment method config name filter * uncomment method config name filter * uncomment method config name filter * uncomment method config name filter * uncomment method config name filter * dont cancel scientific * dont cancel scientific GHA * dont cancel scientific GHA * debugging dont cancel scientific GHA * debugging dont cancel scientific GHA * look for inputs * fix cancel gha * clean up logging * clean up testtype * clean up testtype * clean up testtype * add abort jobs functionality to all tests * fix bug in upload step * fix bug in upload step * rearrange delete and create steps * rearrange delete and create steps * PD-2854: ATAC tests (#1500) * bug fix?? * remove unused variables * remove some more (hopefully) unused variables * remove the rest of the env blocks * add some env vars * add documentation and clean up env vars * revert nested plumbing inputs * revert nested plumbing inputs * hardcode truth paths for snm3c and multisnss2 * refactor illumina arrays * refactor illumina arrays * refactor illumina arrays * refactor illumina arrays * refactor illumina arrays * use METHOD_CONFIG_NAME * refactor all ymls except snm3c and multisnss2 * fix commenting and logging * stop hardcoding snm3c and multisnss2 * commenting * new inputs --------- Co-authored-by: Elizabeth Kiernan <[email protected]> Co-authored-by: jessicaway <[email protected]> Co-authored-by: Robert Sidney Cox <[email protected]> Co-authored-by: GitHub Action <[email protected]>
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testing PR