Develop #137

dweemx · 2020-02-24T14:33:27Z

Clean config parameters b6fe7bf d601947 1f9dcf0
Rename data input parameters bc289fb 100efef
- see Input Data Format docs
Add regress out variable step 923a960 b3ac939
- This step is not performed by default
- see Regress Out Variables docs
Explicitly subset highly variable genes Explicitly subset the variable features scanpy#20
Use by default highly variable genes vib-singlecell-nf/pcacv@b457493
Set clusterOptions to be process specific vib-singlecell-nf/scenic@bd3d1f5
Add progress monitoring for grnboost2 w/o dask vib-singlecell-nf/scenic@bbdd25a
Add case study Kurmangaliyev Y Z et al., 2019 40b092c
Workflows are data input type agnostic Feature/110 workflow data type agnostic #136 Enable h5ad files to be used as inputs to other workflows #110
Workflows are fully reproducible Set a fixed seed for all steps #43
Fix bug unpaired reports (clustering and batch effect correction) c851207 vib-singlecell-nf/scanpy@9b2684c
Fix important bug in mnncorrect pipeline 07ce04c mnnCorrect does not run properly scanpy#22
Update DAGs 2af9ab5
Add new CI for bbknn_scenic pipeline ad6d89f e365d45 468ad10 7b35333 27cb082

Add the 2 config files (bbknn and harmony) Add new section in docs Update the Hung R et al., 2019 case study with correct link

This is not done by default

….cellranger_outs_dir_paths Update docs

Create new config for cellranger h5 files

Create main channels handling all different data input types Update SC__FILE_CONVERTER with the input data type and output data type Hence update and clean main.nf Update RtD

Rename cellranger_h5_file_paths to cellranger_h5 Rename cellranger_outs_dir_paths to cellranger_mex

Plus remove unecessary parameter of h5ad_concatenate.config

…ata_type_agnostic Feature/110 workflow data type agnostic

Pass log-transformed matrices/AnnData objects to mnn_correct, and use HVGs instead of all the genes. (see mnnpy github README)

It seems that mnncorrect does not work with tiny sample_data dataset. The following error is raised: IndexError: index 100 is out of bounds for axis 0 with size 100. Haven't dive into it to understand to real problem

Add link to quick start Add pipelines tags

Use test_TFs_small instead of test_TFs_tiny

dweemx added 30 commits February 20, 2020 14:23

Add case study Kurmangaliyev Y Z et al., 2019

40b092c

Add the 2 config files (bbknn and harmony) Add new section in docs Update the Hung R et al., 2019 case study with correct link

Fix for incorrect input cardinality

d3b277e

Remove redundant prefixes in params

b6fe7bf

Lowercase and remove special chars form the dim reduction method names

d601947

Add regressing out variable step to the pipelines

923a960

This is not done by default

Add profile to regress out vars with scanpy in nextflow.config

b3ac939

Rename params.data.tenx.cellranger_outs_dir_paths to params.data.tenx…

bc289fb

….cellranger_outs_dir_paths Update docs

Add data channel for cellranger h5 files

741d078

Create new config for cellranger h5 files

Implement #110

3df011a

Create main channels handling all different data input types Update SC__FILE_CONVERTER with the input data type and output data type Hence update and clean main.nf Update RtD

Clean configs and main workflows

1f9dcf0

Rename tenx input data params

4185381

Rename cellranger_h5_file_paths to cellranger_h5 Rename cellranger_outs_dir_paths to cellranger_mex

Update input data format in pipelines docs

1dc8db6

Improve docs to define the data input paths

100efef

Fix bug for h5ad data input

879fa68

Plus remove unecessary parameter of h5ad_concatenate.config

Merge pull request #136 from vib-singlecell-nf/feature/110-workflow_d…

87f53e0

…ata_type_agnostic Feature/110 workflow data type agnostic

Add regress out variable docs section

bc04cc8

Populate cell and sample-based docs sections

41300db

Update tools pcacv, scanpy, scenic

7186771

Fix bug cannot find single_sample_standalone

d4919cf

Fix bug unpaired reports (clustering and bec)

c851207

Fix for vibsinglecellnf/scanpy:0.5.0#22

07ce04c

Pass log-transformed matrices/AnnData objects to mnn_correct, and use HVGs instead of all the genes. (see mnnpy github README)

Update tools harmony, scanpy

1d90181

Fix for single_sample pipelines

6b886d1

Fix bug mnncorrect fails with sample_data_tiny dataset

d24fb4a

It seems that mnncorrect does not work with tiny sample_data dataset. The following error is raised: IndexError: index 100 is out of bounds for axis 0 with size 100. Haven't dive into it to understand to real problem

Update DAGs

2af9ab5

Add bbknn_scenic CI

ad6d89f

Update README

81d00c9

Add link to quick start Add pipelines tags

Update scanpy tool

96a4313

Add missing test__bbknn_scenic profile

e365d45

Genome config is required for *scenic pipelines

468ad10

dweemx added 3 commits February 25, 2020 12:24

Use small sample data for bbknn_scenic CI

7b35333

Update log trace in getting-started docs

8ec1851

Update test__bbknn_scenic config

27cb082

Use test_TFs_small instead of test_TFs_tiny

dweemx merged commit f08be71 into master Feb 25, 2020

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Develop #137

Develop #137

dweemx commented Feb 24, 2020 •

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Develop #137

Develop #137

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dweemx commented Feb 24, 2020 • edited Loading

dweemx commented Feb 24, 2020 •

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