Vitessce Pipeline

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 Config_from_paths 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 image_to_zarr 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/v0.1.0If you use this repo, please cite i