Develop #131

dweemx · 2020-02-17T12:17:39Z

Summary of changes

Use fixed seed (by default) for nondeterministic process Feature/43 set seed #129 Set a fixed seed for all steps #43 f439771
Run Cell Ranger using metadata file cab1b73
Neighborhood graph computation has its own process
Finalize mnncorrect pipeline 4d0b89a 97e3b8c
Allow to start the single_sample pipeline with tsv or csv files
Bug fix 07e3f73
Update DAGs a297fc0
Update docs 8190b49

Remove star_concatenator and file_concatenator from base utils config Update main nextflow config accordingly

Create final merge reports Publish final loom Use neighborhood_graph (scanpy) in bbknn pipeline Add to docs to RtD

Create yml config Create test config Add test profile to main nextflow.config

…filtered matrix

Feature/43 set seed

Create configs Rename h5ad channel to file channel since the implementation is generic and will work for csv and tsv Create the (tsv|csv)_single_samples pipelines in main.nf Add data profiles for tsv and csv input data

Update features page with a new section "setting the seed" Update pipelines page with a new sections TSV, CSV

Update cellranger tool

Fix docker formet bug in scenic multiruns configs

dweemx added 18 commits February 14, 2020 13:38

Remove unecessary entries when generating config file

43b3ac9

Remove star_concatenator and file_concatenator from base utils config Update main nextflow config accordingly

Use neighborhood_graph from scanpy in single_sample pipeline

c18c557

Use neighborhood_graph (scanpy) in single_sample_star pipeline

64f7cde

Use neighborhood_graph (scanpy) in bbknn pipeline

43573e0

Use neighborhood_graph (scanpy) in harmony pipeline

58d443f

Finalize mnncorrect pipeline

4d0b89a

Create final merge reports Publish final loom Use neighborhood_graph (scanpy) in bbknn pipeline Add to docs to RtD

Add testing for mnncorrect pipeline through GitHub Actions

97e3b8c

Create yml config Create test config Add test profile to main nextflow.config

Update DAGs

a297fc0

Fix bug cluster_markers row attributes should use all genes from raw …

07e3f73

…filtered matrix

Inform user on seed set by default

2889005

Merge pull request #129 from vib-singlecell-nf/feature/43-set_seed

05fd734

Feature/43 set seed

Update pcacv, scanpy, scenic #43

f439771

Implement #96 for single_sample pipeline

981677d

Create configs Rename h5ad channel to file channel since the implementation is generic and will work for csv and tsv Create the (tsv|csv)_single_samples pipelines in main.nf Add data profiles for tsv and csv input data

Improve renaming samples when downloading SRA

4baa461

Add docs to RtT

8190b49

Update features page with a new section "setting the seed" Update pipelines page with a new sections TSV, CSV

Add workflow and profiles for vib-singlecell-nf/cellranger#1

cab1b73

Update cellranger tool

Update scenic tool

68d5e2a

Fix docker formet bug in scenic multiruns configs

Bump version from 0.10.0 to 0.11.0

74cdd7d

dweemx merged commit dde2a7f into master Feb 17, 2020

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Develop #131

Develop #131

dweemx commented Feb 17, 2020

Develop #131

Develop #131

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dweemx commented Feb 17, 2020