webatlas-pipeline - 0.5.3

What's Changed

• Fix bioformats2raw versions across environments by @StasMakarchuk in https://github.com/haniffalab/webatlas-pipeline/pull/149

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.5.2...v0.5.3

- Python
Published by prete over 1 year ago

webatlas-pipeline - 0.5.2

What's Changed

• Update docs by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/128
• update docs by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/129
• update docs by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/130
• Patch for Xenium software analyzer >= 2.0.0 by @prete in https://github.com/haniffalab/webatlas-pipeline/pull/131
• fix singularity profile by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/133
• 0.5.2 by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/134

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.5.1...v0.5.2

- Python
Published by davehorsfall over 1 year ago

webatlas-pipeline - 0.5.1

What's Changed

• Create release 0.5.1 by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/127

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.5.0...v0.5.1

- Python
Published by dannda about 2 years ago

webatlas-pipeline - 0.5.0

What's Changed

• Feat/write spatialdata by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/121
• Feat/multimodal by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/125
• Create release 0.5.0 by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/126

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.4.1...v0.5.0

- Python
Published by davehorsfall about 2 years ago

webatlas-pipeline - 0.4.1

What's Changed

• Split and organise environment and container files by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/115
• split sphinx actions to build and deploy by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/118
• add documentation on multimodal pipeline by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/116
• Create release 0.4.1 by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/119

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.4.0...v0.4.1

- Python
Published by davehorsfall over 2 years ago

webatlas-pipeline - 0.4.0

What's Changed

• Add support for Xenium 1.3 outputs by @prete in https://github.com/haniffalab/webatlas-pipeline/pull/90
• add parameter to load raw count file from spaceranger output by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/91
• add consolidatemetadata param to processh5ad by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/92
• update dev branch from main by @BioinfoTongLI in https://github.com/haniffalab/webatlas-pipeline/pull/94
• added conda env as an option by @BioinfoTongLI in https://github.com/haniffalab/webatlas-pipeline/pull/93
• Improve documentation by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/101
• Multimodal test by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/107
• Resolve Multimodal support for pipeline by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/97
• Create release 0.4.0 by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/112

New Contributors

• @prete made their first contribution in https://github.com/haniffalab/webatlas-pipeline/pull/90

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.3.2...v0.4.0

- Python
Published by davehorsfall over 2 years ago

webatlas-pipeline - 0.3.2

What's Changed

• Bump 0.3.1 by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/86
• add license to close #87 by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/88
• Add license by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/89

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.3.1...v0.3.2

- Python
Published by davehorsfall almost 3 years ago

webatlas-pipeline - 0.3.1

What's Changed

• Upgrade build config by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/85
• load Xenium clustering into h5ad file by @BioinfoTongLI in https://github.com/haniffalab/webatlas-pipeline/pull/74

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.3.0...v0.3.1

- Python
Published by davehorsfall almost 3 years ago

webatlas-pipeline - 0.3.0

What's Changed

• Manuscript prep by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/73
• turn input path strings to file type by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/81
• add check for 'options' when adding files to view config by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/82
• Update process_spaceranger.py by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/83
• Prep version bump by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/84

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.2.0...v0.3.0

- Python
Published by davehorsfall almost 3 years ago

webatlas-pipeline - 0.2.0

What's Changed

• add batch processing option to process_h5ad.py by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/47
• Docs and citation by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/55
• Refactor by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/56
• Feat/add technologies by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/61
• multimodal draft v1 by @BioinfoTongLI in https://github.com/haniffalab/webatlas-pipeline/pull/66
• Multimodal integration by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/68
• Refactor to yaml input by @dannda in https://github.com/haniffalab/webatlas-pipeline/pull/69
• Preparation for WebAtlas manuscript by @davehorsfall in https://github.com/haniffalab/webatlas-pipeline/pull/70

Full Changelog: https://github.com/haniffalab/webatlas-pipeline/compare/v0.1.0...v0.2.0

- Python
Published by davehorsfall almost 3 years ago

webatlas-pipeline - 0.1.0

What's Changed

• data conversion pipeline using nextflow by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/2
• Nextflow by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/3
• make the h5ad conversion a two-step process; updated the future plan … by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/7
• added check for files for config file in python by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/9
• added factors list to params by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/10
• Feat/anndata to zarr by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/12
• Feat/config api by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/17
• Updates by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/23
• codebook added; parsing channel names with python xml by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/24
• added Configfrompaths workflow by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/25
• Merged new build_config changes; Introduced breaking changes about input data parsing by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/26
• Feat/scrnaseq pipeline by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/28
• s3 data support; conda file cleanup by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/29
• added version tagging and citation information by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/31
• fixed Config workflow given updated Build_config process by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/32
• added python tests with pytest by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/33
• Update README.md by @iolosquires in https://github.com/haniffalab/vitessce-pipeline/pull/34
• add codecov upload by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/36
• add coverage flag value by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/37
• add badges to README by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/38
• convert spaceranger output into anndata.zarr; minor change about relative script import; version tagging by @BioinfoTongLI in https://github.com/haniffalab/vitessce-pipeline/pull/39
• Fix process h5ad by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/42
• fixes issue #40 in reading spot ids by @iolosquires in https://github.com/haniffalab/vitessce-pipeline/pull/43
• Refactor by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/44
• add step to uncompressed jpeg-compressed tif images in imagetozarr by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/46
• Dev by @dannda in https://github.com/haniffalab/vitessce-pipeline/pull/48
• Prep 0.1.0 by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/49
• Automation workflows by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/50
• Codecov by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/51
• Prep 0.1.0 by @davehorsfall in https://github.com/haniffalab/vitessce-pipeline/pull/52

New Contributors

• @BioinfoTongLI made their first contribution in https://github.com/haniffalab/vitessce-pipeline/pull/2
• @davehorsfall made their first contribution in https://github.com/haniffalab/vitessce-pipeline/pull/3
• @dannda made their first contribution in https://github.com/haniffalab/vitessce-pipeline/pull/9
• @iolosquires made their first contribution in https://github.com/haniffalab/vitessce-pipeline/pull/34

Full Changelog: https://github.com/haniffalab/vitessce-pipeline/commits/v0.1.0

- Python
Published by davehorsfall about 3 years ago