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Display the command used to launch docker from lambda #63

Merged
merged 1 commit into from
May 19, 2021
Merged

Display the command used to launch docker from lambda #63

merged 1 commit into from
May 19, 2021

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xverges
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@xverges xverges commented May 11, 2021

Minor changes.

@xverges xverges merged commit b48ae80 into develop May 19, 2021
@xverges xverges deleted the show-docker-command branch May 19, 2021 07:02
kafkasl pushed a commit that referenced this pull request Jun 15, 2021
@xverges @kafkasl
Display the command used to launch docker from lambda (#63)
508c882
kafkasl added a commit that referenced this pull request Jun 17, 2021
@kafkasl @alexvpickering
@ogibson @JuanluOnieva-biomage @dependabot @seb-mueller @xverges @aerlaut @cosa65 @robioson
Merge master into dev branch (#100)
831c27b 
* handle NA doublet scores (#61)

* Added no integration (#59)

* Added no integration

* Update qc-runner/src/dataIntegration.r

Co-authored-by: Juanlu <[email protected]>

Co-authored-by: Juanlu <[email protected]>

* 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] <[email protected]>

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] <[email protected]>

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 <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>

* Dependency issues and cellsets (#65)

Co-authored-by: Oliver Gibson <[email protected]>

* Add sns updates when tasks finish (#67)

Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Xavier Verges <[email protected]>

* Handle gem2s response refactoring (#68)

* Add sns updates when tasks finish

* Handle gem2s response refactoring

* Minor renaming

* Fix

* Fix

Co-authored-by: Martin Fosco <[email protected]>

* [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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>

* [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 <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>
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 <[email protected]>

Co-authored-by: Juanlu <[email protected]>

* 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] <[email protected]>

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] <[email protected]>

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 <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>

* Dependency issues and cellsets (#65)

Co-authored-by: Oliver Gibson <[email protected]>

* Add sns updates when tasks finish (#67)

Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Xavier Verges <[email protected]>

* Handle gem2s response refactoring (#68)

* Add sns updates when tasks finish

* Handle gem2s response refactoring

* Minor renaming

* Fix

* Fix

Co-authored-by: Martin Fosco <[email protected]>

* [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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>

* [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 <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* fixes

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Alex Pickering <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* 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 <[email protected]>

* Fix (#113)

* Fix

* typo

Co-authored-by: Oliver Gibson <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* 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 <[email protected]>

Co-authored-by: Alex Pickering <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: StefanBabukov <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: Marcell Pek <[email protected]>
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 <[email protected]>

Co-authored-by: Juanlu <[email protected]>

* 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] <[email protected]>

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] <[email protected]>

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 <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>

* Dependency issues and cellsets (#65)

Co-authored-by: Oliver Gibson <[email protected]>

* Add sns updates when tasks finish (#67)

Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Xavier Verges <[email protected]>

* Handle gem2s response refactoring (#68)

* Add sns updates when tasks finish

* Handle gem2s response refactoring

* Minor renaming

* Fix

* Fix

Co-authored-by: Martin Fosco <[email protected]>

* [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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>

* [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 <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* fixes

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Alex Pickering <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* 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 <[email protected]>

* Fix (#113)

* Fix

* typo

Co-authored-by: Oliver Gibson <[email protected]>

* 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 <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* fix empty guidata case

Co-authored-by: Juanlu <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: StefanBabukov <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: Marcell Pek <[email protected]>
alexvpickering pushed a commit that referenced this pull request Dec 8, 2022
@cosa65
Merge pull request #63 from biomage-org/2241-pipeline-pass-url
0c2cdc6 
[2241] send apiUrl in the sns message
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