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Init filter high mito and filter gene umi outlier tests #114

Merged
merged 3 commits into from Jul 1, 2021
Merged

Init filter high mito and filter gene umi outlier tests #114

merged 3 commits into from Jul 1, 2021

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alexvpickering
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Background

Link to issue

https://biomage.atlassian.net/secure/RapidBoard.jspa?rapidView=1&modal=detail&selectedIssue=BIOMAGE-1129

Link to staging deployment URL

Links to any Pull Requests related to this

Anything else the reviewers should know about the changes here

Changes

Code changes

Definition of DONE

Your changes will be ready for merging after each of the steps below have been completed:

Testing

  • Unit tests written
  • Tested locally with Rstudio (tests pass)
  • Deployed to staging

To set up easy local testing with inframock, follow the instructions here: https://github.com/biomage-ltd/inframock
To deploy to the staging environment, follow the instructions here: https://github.com/biomage-ltd/biomage-utils

Documentation updates

Is all relevant documentation updated to reflect the proposed changes in this PR?

  • Relevant Github READMEs updated
  • Relevant wiki pages created/updated

Approvers

  • Approved by a member of the core engineering team
  • (UX changes) Approved by vickymorrison (this is her username, tag her if you need approval)

Just before merging:

Optional

  • Photo of a cute animal attached to this PR

@alexvpickering alexvpickering merged commit 5f166ad into develop Jul 1, 2021
@alexvpickering alexvpickering deleted the init-gumi-tests branch July 1, 2021 22:28
ivababukova pushed a commit that referenced this pull request Jul 19, 2021
@kafkasl @alexvpickering
@JuanluOnieva-biomage @ogibson @dependabot @seb-mueller @xverges @aerlaut @cosa65 @robioson @StefanBabukov @marcellp
Release version 0.0.2 (#120)
4372389 
* add harmony integration (#98)

* add harmony

* refactor

* remove mistakes

* add dispersions for harmony

* Fix p.level (#102)

* Merge master into dev branch (#100)

* 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>

* done i think (#101)

* Add build as a dependency of run (#103)

Also add new run-only target

* Init R package and test classifier filter (#104)

* 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

* Enable Slack build failure notifications

* Fix defaults (#109)

Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>

* Unlog y values (#112)

* unlog cellsizedistribution plot y values
* switch plot numbers to improve readibility

* Clean pipeline code (#105)

* 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 high mito and filter gene umi outlier tests (#114)

* init filter_gene_umi_outlier tests

* init mito filter tests; fix calc_filter_stats

* Init cellszdoublet tests (#118)

* 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 (#107)

* 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>

* Fix (#113)

* Fix

* typo

Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>

* init renv (#110)

* 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>

* Move defaultFilterSettings and missing per sample config additions to 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>

Co-authored-by: Alex Pickering <alexvpickering@gmail.com>
Co-authored-by: Juanlu <76958039+JuanluOnieva-biomage@users.noreply.github.com>
Co-authored-by: ogibson-biomage <76957896+ogibson-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>
Co-authored-by: StefanBabukov <stefanbabukov98@gmail.com>
Co-authored-by: James Robinson <james@biomage.net>
Co-authored-by: Marcell Pek <marcell.pek@marcellp.net>
ivababukova pushed a commit that referenced this pull request Jul 20, 2021
@alexvpickering @JuanluOnieva-biomage
@kafkasl @ogibson @dependabot @seb-mueller @xverges @aerlaut @cosa65 @robioson @StefanBabukov @marcellp
Hotfix/fix master (#122)
c06d01f 
* add harmony integration (#98)

* add harmony

* refactor

* remove mistakes

* add dispersions for harmony

* Fix p.level (#102)

* Merge master into dev branch (#100)

* 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>

* done i think (#101)

* Add build as a dependency of run (#103)

Also add new run-only target

* Init R package and test classifier filter (#104)

* 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

* Enable Slack build failure notifications

* Fix defaults (#109)

Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>

* Unlog y values (#112)

* unlog cellsizedistribution plot y values
* switch plot numbers to improve readibility

* Clean pipeline code (#105)

* 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 high mito and filter gene umi outlier tests (#114)

* init filter_gene_umi_outlier tests

* init mito filter tests; fix calc_filter_stats

* Init cellszdoublet tests (#118)

* 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 (#107)

* 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>

* Fix (#113)

* Fix

* typo

Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>

* init renv (#110)

* 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>

* Move defaultFilterSettings and missing per sample config additions to 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>

* init density kneeplot data (#111)

* init density kneeplot data

* update plot

* use unique fdr/ranks

* get_bcranks_plot_data works

* fix

* Fix

* Rollback unnecessary empty plot data addition

Co-authored-by: Oliver Gibson <olivergibson@MacBook-Pro-de-Oliver.local>
Co-authored-by: Martin Fosco <martinfosco@Martins-MacBook-Pro.local>

* fix empty guidata case

Co-authored-by: Juanlu <76958039+JuanluOnieva-biomage@users.noreply.github.com>
Co-authored-by: Pol Alvarez <pol.avms@gmail.com>
Co-authored-by: ogibson-biomage <76957896+ogibson-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>
Co-authored-by: StefanBabukov <stefanbabukov98@gmail.com>
Co-authored-by: James Robinson <james@biomage.net>
Co-authored-by: Marcell Pek <marcell.pek@marcellp.net>
alexvpickering pushed a commit that referenced this pull request Feb 7, 2023
@cosa65
Merge pull request #114 from biomage-org/patch-ensure-cell-ids-are-li…
957f276 
…st-in-cell-sets

Patch, ensure `cellIds` is sent as an array always
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