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haniffalab / webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
MIT License
46 stars 10 forks source link

load Xenium clustering into h5ad file #74

Closed BioinfoTongLI closed 1 year ago

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage has no change and project coverage change: -0.17 :warning:

Comparison is base (fe507fd) 37.17% compared to head (edd0c02) 37.01%.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #74 +/- ## ========================================== - Coverage 37.17% 37.01% -0.17% ========================================== Files 14 14 Lines 694 697 +3 ========================================== Hits 258 258 - Misses 436 439 +3 ``` | [Impacted Files](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/74?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab) | Coverage Δ | | |---|---|---| | [bin/build\_config.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/74?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2J1aWxkX2NvbmZpZy5weQ==) | `0.00% <ø> (ø)` | | | [bin/process\_xenium.py](https://codecov.io/gh/haniffalab/webatlas-pipeline/pull/74?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfeGVuaXVtLnB5) | `32.65% <0.00%> (-2.13%)` | :arrow_down: |

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BioinfoTongLI commented 1 year ago

looks like an doc action deployment issue?

davehorsfall commented 1 year ago

The reason the deploy action fails is because you're merging from a fork of the repo, not a branch - so you don't have permission to deploy to the docs from your forked repo.

BioinfoTongLI commented 1 year ago

not really. Especially you said that the 10x Xenium dataset is working well with the current version. We can come back to this after biorXiv submission

dannda commented 1 year ago

Current version was not loading embeddings and clusters so we do need to merge this. I've dded logic similar to processing spaceranger to load all clusters and embeddings.