Release version 0.0.2 #120
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* add harmony * refactor * remove mistakes * add dispersions for harmony
* handle NA doublet scores (#61) * Added no integration (#59) * Added no integration * Update qc-runner/src/dataIntegration.r Co-authored-by: Juanlu <76958039+JuanluOnieva-biomage@users.noreply.github.com> Co-authored-by: Juanlu <76958039+JuanluOnieva-biomage@users.noreply.github.com> * Bump lodash from 4.17.20 to 4.17.21 in /local-runner (#58) Bumps [lodash](https://github.com/lodash/lodash) from 4.17.20 to 4.17.21. - [Release notes](https://github.com/lodash/lodash/releases) - [Commits](lodash/lodash@4.17.20...4.17.21) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump hosted-git-info from 2.8.8 to 2.8.9 in /local-runner (#64) Bumps [hosted-git-info](https://github.com/npm/hosted-git-info) from 2.8.8 to 2.8.9. - [Release notes](https://github.com/npm/hosted-git-info/releases) - [Changelog](https://github.com/npm/hosted-git-info/blob/v2.8.9/CHANGELOG.md) - [Commits](npm/hosted-git-info@v2.8.8...v2.8.9) Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Na doublet score (#62) * handle NA doublet scores * treat NA as doublet_score=0 * Add FastMNN step 6-7 (#60) * Add FastMNN step 6-7 * Fix dockerfile * Fix scdata * change order * Fix try-catch * Change value to unisample and fastmnn * Fix assay * Add package * Add dependencies * Change to pak * Add active.reduciton and pak * Add var.explained * Add comments * Persist misc * added improved error handling and traceback (#55) * added improved error handling and traceback * removed dump.frames * no sample output for integration step * moved state_fail_logic to withCallingHandlers block * removed intended debug error * Display the command used to launch docker from lambda (#63) * Move GEM2S as a step in pipeline (#56) * refactor wrapper * Added gem2s functions to pipeline * Adapted pipeline to new schema for gem2s * renamed one task * fixes for gem2s * renamed qc-runner to pipeline-runner * fixed tryCatch from rebase * changed pipeline name to qc * init upload-to-aws * init meta_sets * Added sample sets * complete upload-to-aws * add s3/dynamodb functions * add buckets and tables * writing input to meta.json file * changed some pipeline references to gem2s/pipeline * avoiding creating new containers for gem2s or qc if they already exist * attaching both pipeline containers output (qc & gem2s) to pipeline process stdout * just a lonenly runaway letter * added dependencies * typo * make docker build for me * send dynamodb items to api * reflect nan bugfix from data-inegest * temporarily fix for paws.common version 0.3.11 * change SNS messag type * hotfix * fix * fix Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> Co-authored-by: Pol Alvarez <pol.avms@gmail.com> Co-authored-by: Anugerah Erlaut <aerlaut@live.com> * Dependency issues and cellsets (#65) Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> * Add sns updates when tasks finish (#67) Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local> * fix per sample custom config (#66) * fix per sample custom config * loop through unique samples * Fix seurat obj not found (#71) * Sample ids property sent as list instead of string * fix seurat_obj not found Co-authored-by: Martin Fosco <martinfosco@192.168.1.7> Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> Co-authored-by: Xavier Verges <460418+xverges@users.noreply.github.com> * Handle gem2s response refactoring (#68) * Add sns updates when tasks finish * Handle gem2s response refactoring * Minor renaming * Fix * Fix Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local> * [BIOMAGE-1016] Sample uuids fix (#72) * Sample ids property sent as list instead of string * Fix * Draft fix for uuids * Fix * fix * fix * checks Co-authored-by: Martin Fosco <martinfosco@192.168.1.7> Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local> * Fix fast mnn (#75) * Sample ids property sent as list instead of string * Add FastMNN * Restore 5_Upload-to-aws * [BIOMAGE-1040] - Fix metadata structures (#74) * fix data structures * fix for empty metadata Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> * [BIOMAGE-1009] Fix error sns messages (#73) * Refactor and add method dedicated to only sending sns error messages * Add experimentId * Move classifier to current position in ui * Move into one single line Co-authored-by: Martin Fosco <martinfosco@192.168.1.7> Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local> * Add experimentID and ingestionDate (#77) * Add experimentID and ingestionDate * Update comment * Init filter stats (#76) * init calc_filter_stats * add filter stats for cellSizeDistribution * return filter stats for all filter steps * Test * restore spacing for ease * revert * reverting spacing changes * more de-change * fix conflict * check samples Co-authored-by: Martin Fosco <martinfosco@192.168.1.7> * move code from data-ingest (#78) * fix mtcontent plotdata error (#79) * new flow for releases (#83) * added deployment for release/hotfixes PRs to master (#85) * using tokens to allow flow to trigger testing * Fix doublet settings (#81) * test doublet settings * Fix error in doublet scores config Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> * building releases/hotfixes on PR instead of push * Fix determination of HOST_IP on Linux (#91) * Fix determination of HOST_IP on Linux * Replace spaces with tab * Add tty flag to fix local output (#92) * Update ci-develop.yaml * Fix default doublet config (#82) * use seed and fix config storage * use scDblFinder to set default threshold * remove gitignore * remove debug * change boolean logic * Rm auto and enabled (#88) * switch from orig.ident to samples (#95) * Move to multipart upload (#94) * Move to multipart upload * Add print * Fix progress-bar * hardcode DEBUG_PATH (#93) * hardcode DEBUG_PATH * fix function name * Remove hardcoded 10x (it is now hardcoded in the ui only) (#96) Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local> * re-enable per sample config (#97) * added r.utils dependency install which is required by seurat-wrappers (#99) * Deprecated change for ci.yaml Co-authored-by: Alex Pickering <alexvpickering@gmail.com> Co-authored-by: ogibson-biomage <76957896+ogibson-biomage@users.noreply.github.com> Co-authored-by: Juanlu <76958039+JuanluOnieva-biomage@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: seb-mueller <sebm@posteo.de> Co-authored-by: Xavier Vergés <460418+xverges@users.noreply.github.com> Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> Co-authored-by: Anugerah Erlaut <aerlaut@live.com> Co-authored-by: Martin Fosco <cosa65@users.noreply.github.com> Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local> Co-authored-by: Anugerah Erlaut <anugerah@biomage.net> Co-authored-by: Martin Fosco <martinfosco@192.168.1.7> Co-authored-by: James Robinson <robioson@pm.me>
Also add new run-only target
* init r package * ignore debug * remove file names within file * use styler * cleanup * fix Dockerfile * init filter_emptydrops tests * fix introduced error for demo image * add sample aware test * update README; make task names look distinct * update README * update gem2s step messages * add timer to gem2s steps
Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>
* unlog cellsizedistribution plot y values * switch plot numbers to improve readibility
* Clean pipeline code * Update pipeline-runner/R/gem2s-6-prepare_experiment.R Co-authored-by: Alex Pickering <alexvpickering@gmail.com> * Update pipeline-runner/R/gem2s-helpers.R Co-authored-by: Alex Pickering <alexvpickering@gmail.com> * Update pipeline-runner/R/gem2s-helpers.R * Update pipeline-runner/R/gem2s-helpers.R Co-authored-by: Alex Pickering <alexvpickering@gmail.com> * fixes * Update pipeline-runner/R/gem2s-helpers.R Co-authored-by: Alex Pickering <alexvpickering@gmail.com> Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local> Co-authored-by: Alex Pickering <alexvpickering@gmail.com>
* init filter_gene_umi_outlier tests * init mito filter tests; fix calc_filter_stats
* init filter_gene_umi_outlier tests * init mito filter tests; fix calc_filter_stats * Added tests for cellsize and doublets * export filter_low_cellsize * simplify parts of filter_low_cellsize * restyle and update comment for filter_doublets test * fix filter_doublets documentation Co-authored-by: Alex Pickering <alexvpickering@gmail.com> Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>
* Removed embedding * Update pipeline-runner/R/qc-7-embed_and_cluster.R * Update pipeline-runner/R/qc-7-embed_and_cluster.R * Update pipeline-runner/R/qc-7-embed_and_cluster.R * Fix Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>
* try restore remoter docker-compose * Update pipeline-runner/renv.lock.init * Update pipeline-runner/renv.lock * try update all packages * Fix * update README; remove R version * harmony init lockfile * fix Co-authored-by: ogibson-biomage <76957896+ogibson-biomage@users.noreply.github.com> Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>
… the pipeline (#119) * Add defaultFilterSettings and per sample config for classifier and mito content * Update gem2s-6-prepare_experiment.R Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local>
ivababukova
approved these changes
Jul 19, 2021
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This PR was created in response to a manual trigger of the release workflow here: https://github.com/biomage-ltd/pipeline/actions/runs/1023154669.
Merging this PR will create a GitHub release, update master & develop branches, and upload any assets that are created as part of the release build.