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

Refactor to yaml input #69

Closed dannda closed 1 year ago

dannda commented 1 year ago

Refactor to use a single yaml file as user input instead of yaml + csv

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (766357e) 37.58% compared to head (d57df32) 37.58%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #69 +/- ## ======================================= Coverage 37.58% 37.58% ======================================= Files 14 14 Lines 697 697 ======================================= Hits 262 262 Misses 435 435 ``` | [Impacted Files](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/69?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab) | Coverage Δ | | |---|---|---| | [bin/process\_h5ad.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/69?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfaDVhZC5weQ==) | `85.34% <ø> (ø)` | | | [bin/process\_xenium.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/69?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfeGVuaXVtLnB5) | `34.78% <ø> (ø)` | | | [bin/process\_merscope.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/69?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfbWVyc2NvcGUucHk=) | `23.68% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab)

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.