Develop #238

dweemx · 2020-10-21T13:19:25Z

Summary

Bump version from 0.20.0 to 0.21.0
Merge Feature/228 support for celda decontx #230 Closes [NEW TOOL] Add support for DecontX #228 Add DecontX
Merge Feature/229 support for soupx #237 Closes [NEW TOOL] Add support for SoupX #229 Add SoupX
Closes [SUGGESTION] Improve interoperability with Scanpy #233 3a66a0c Improve interoperability with Scanpy
Closes [SUGGESTION] Merge final h5ad files when in param exploration mode #234 Merge final h5ad files when in param exploration mode
Closes [SUGGESTION] Store log files in log folder #235 Store log files in log folder
c1cf114 Support for h5ad built with anndata>=0.7.x for h5ad to loom conversion
Bug fixes [BUG] sample_id not added when running pipeline from "seurat_rds" #227 [BUG] h5ad_to_loom.py has help='The name of the genome.' for multiple parameters. #236
Bug fix 0bbffbc Regressing out variables should be performed after HVG and before feature scaling
New label for report NXF processes: compute_resources__report
[scenic] 455a165 Allow to use --all_modules argument when running the cisTarget step
[scanpy] 06f4a41 Fix bug cells not matching when running mnncorrect batch effect correction pipeline

…g the Nextflow command

- Increase max size of object to share with future package from 1Gb to 2Gb - Free up memory by removing vars and calling gc

Bug fix for misspelled n-cores flag

…al in sc_file_converter.R

…lti-sample parameter feature

…et step

…esources__report' and label all process that generate reports with 'compute_resources__report'

… params.sc.file_converter.off Update add off param and set it to seurat_rds in tenx_atac_cellranger_mex.config

…r the file converter to use

Improve code in SC__FILE_CONVERTER process

…iltering This regards the SC__PREPARE_OBS_FILTER and SC__APPLY_OBS_FILTER processes

…e.g.: h5ad): SC__FILE_CONVERTER_FROM_SCE Plus remove unused process SC__FILE_CONVERTER_HELP

…. This allows to have multiple SC__FILE_CONVERTER with different output formats running within 1 pipeline.

…lParams instead of the toolKey

…config: run single_sample_scrublet along with decontx [celda] pipelines. The scrublet workflow is applied on the DecontX filtered data.

…rting 10x_cellranger_mex to sce_rds. And add logic for tagging the cell with sample id for that conversion.

…pipeline both with Scrublet and DecontX data

pcacv: Minor changes scrublet: Check for NA values and fill them so that num doublets can be calculated at end of notebook

…r_soupx Feature/229 support for soupx

…ture scaling (see https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html)

The Scanpy-ready are generated for the following pipelines: - harmony* - bbknn* - mnncorrect - single_sample* - multi_sample

…ample nxf workflow)

…ICATION in single_sample.nf

…econtx_correct, test__single_sample_decontx_correct_scrublet Plus typo fix

… are not using AnnData.concatenate

…ect correction i.e.: cells not matching between BEC_MNNCORRECT.out.data and SC__FILE_CONCATENATOR.out when running FINALIZE in mnncorrect workflow

dweemx added 30 commits October 1, 2020 10:16

Update prerequisite docs: LANG and LC_ALL should be set before runnin…

f9b364c

…g the Nextflow command

Update pcacv

e8e2648

- Increase max size of object to share with future package from 1Gb to 2Gb - Free up memory by removing vars and calling gc

Update pcacv tool

b9cd530

Bug fix for misspelled n-cores flag

Fixes #227

14a86ee

Add sanity check when columns of seurat@meta.data are not 1-dimension…

3489679

…al in sc_file_converter.R

Update docs describing how to use a "general" param when using the Mu…

84ce9f5

…lti-sample parameter feature

Fix typo

08a06c3

[scenic] Allow to use --all_modules argument when running the cisTarg…

455a165

…et step

[scenic] Fix argument naming

35535ab

[scanpy] Computing dimensionality reduction is cpu intensive

c812a9c

[scanpy,scenic,scrublet] Create new compute resource label 'compute_r…

2e5881f

…esources__report' and label all process that generate reports with 'compute_resources__report'

[scrublet] Update

47c0ab8

Add celda submodule

638121a

[channels] By default output format is h5ad otherwise it's defined by…

1818a0c

… params.sc.file_converter.off Update add off param and set it to seurat_rds in tenx_atac_cellranger_mex.config

Improve scriipt of SC__FILE_CONVERTER by using helper closure to infe…

64cf85e

…r the file converter to use

[utils] Switch to arparse and retab in sc_file_converter.R

2fe4b1c

[utils] Add support for converting from 10x_cellranger_mex to Rds

bd312c9

Improve code in SC__FILE_CONVERTER process

[utils] Allow to use a nested key when tool is doing the cell-based f…

c24fe92

…iltering This regards the SC__PREPARE_OBS_FILTER and SC__APPLY_OBS_FILTER processes

Add printMap helper function to print Map as a prettified JSON

ca31f92

[utils] getContainer should use params in SC__FILE_CONVERTER process

f42cc17

[utils] Add new process to convert from SingleCellExperiment to ... (…

1788627

…e.g.: h5ad): SC__FILE_CONVERTER_FROM_SCE Plus remove unused process SC__FILE_CONVERTER_HELP

Fix typo in compute_resources.config

85182b0

[channels] Allows to use getDataChannel dynamically (i.e.: addParams)…

bfbc8d7

…. This allows to have multiple SC__FILE_CONVERTER with different output formats running within 1 pipeline.

[utils] Value at given toolKey in params should be returned in getToo…

eafe2e4

…lParams instead of the toolKey

[utils] Use getToolParams in ANNOTATE_BY_CELL_METADATA

81cceac

Add single_sample_decontx_filter_scrublet pipeline and corresponding …

b9a65b6

…config: run single_sample_scrublet along with decontx [celda] pipelines. The scrublet workflow is applied on the DecontX filtered data.

[utils] Fix bug cell names not set in SinlgeCellExperiment when conve…

1f0c410

…rting 10x_cellranger_mex to sce_rds. And add logic for tagging the cell with sample id for that conversion.

[utils] Add support to annotate the h5ad with multiple metadata files

42dd005

Annotate the final loom of the single_sample_decontx_filter_scrublet …

c6f98d6

…pipeline both with Scrublet and DecontX data

Update scrublet, pcacv

b2cdd08

pcacv: Minor changes scrublet: Check for NA values and fill them so that num doublets can be calculated at end of notebook

dweemx added 29 commits October 19, 2020 17:16

Merge pull request #237 from vib-singlecell-nf/feature/229-support_fo…

bd44086

…r_soupx Feature/229 support for soupx

Regressing out variables should be performed after HVG and before fea…

0bbffbc

…ture scaling (see https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html)

Closes #236

95a5d33

Support for h5ad built with anndata>=0.7.x in h5ad to loom conversion

c1cf114

Closes #233 #234

4fbd41a

The Scanpy-ready are generated for the following pipelines: - harmony* - bbknn* - mnncorrect - single_sample* - multi_sample

[celda] Pass the seed argument to celda::decontX in run_decontx.R

5deff1f

[scanpy] Missing argument when calling INIT in main.nf

2b70c2d

Missing argument when calling INIT in main_atac.nf

f3376df

Return not required in INIT from utils.nf

54f7369

Closes #235

66c22b7

[celda, soupx] Rebase develop onto master

7c17c3c

Add output files table for bbknn, bbknn_scenic, harmony and mnncorrect

3a66a0c

[scanpy] Fix bug wrong input into DIM_REDUCTION_PCA process (single_s…

9e9fc33

…ample nxf workflow)

Add missing FINALIZE import

802adce

Add single_sample_decontx_correct profile

bf25783

Use DecontX correct strategy for single_sample_decontx* CI

035e263

[scanpy] Fix bug transformed_normalized not found for CLUSTER_IDENTIF…

031a8ec

…ICATION in single_sample.nf

[scanpy] Add missing FINALIZE in single_sample.nf

06047e3

Rename celda_decontx to decontx and use correct strategy for decontx CI

c61a494

Compress and publish only if fileOutputSuffix is not null

8fe1169

Missing scanpyh5ad channel output in single_sample.nf pipeline

b5e45eb

Add missing test configs for CI: test__decontx, test__single_sample_d…

c9e0102

…econtx_correct, test__single_sample_decontx_correct_scrublet Plus typo fix

[celda] Restore main.nf to vib-singlecell-nf/celda#0b5adbd

2e2b7b1

Rename test configs

8168751

[celda] DecontX requires a inherent cell_annotate config

1427968

Join argument is not required anymore in in sc_h5ad_merge.py since we…

56bf57e

… are not using AnnData.concatenate

[scanpy] Fix bug cells not matching when running mnncorrect batch eff…

06f4a41

…ect correction i.e.: cells not matching between BEC_MNNCORRECT.out.data and SC__FILE_CONCATENATOR.out when running FINALIZE in mnncorrect workflow

Only create new symlink if outputFileName does not exist

37cbfbb

Bump version from 0.20.0 to 0.21.0

878e223

dweemx merged commit 1edc521 into master Oct 22, 2020

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Develop #238

Develop #238

dweemx commented Oct 21, 2020 •

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Develop #238

Develop #238

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dweemx commented Oct 21, 2020 • edited Loading

Summary

dweemx commented Oct 21, 2020 •

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