Add new module stainwarpy/extractchannel#9776
Conversation
tckumarasekara
force-pushed
the
pr-extractchannel
branch
from
dcb0855 to
fc3fe6f
Compare
tckumarasekara
changed the title
itrujnara
left a comment
itrujnara
left a comment
There was a problem hiding this comment.
Hi, the module already looks quite good. I have left some questions to consider. They probably apply to the other subcommand modules as well.
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| file(process.out.single_ch_image.get(0).get(1)).exists(), |
There was a problem hiding this comment.
Is the file in question indeterministic? Is there any data in the channel that is not checked here?
There was a problem hiding this comment.
Hi, yes, the output file is non-deterministic between runs due to metadata (ef: UUIDs) and minor floating-point differences. This is the case for the other modules also. This module emits just one file in a tuple.
| type: file | ||
| description: Single channel extracted image file in OME-TIFF format | ||
| pattern: "multiplexed_single_channel_img.ome.tif" | ||
| ontologies: [] |
There was a problem hiding this comment.
Is this the correct ontology?
https://edamontology.github.io/edam-browser/#format_3727
Keep in mind that there have been some issues with the ontology server, so linting/CI might misbehave.
There was a problem hiding this comment.
Yes, thank you. I`ll update the meta.yml
| label 'process_single' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "community.wave.seqera.io/library/stainwarpy:0.2.3--2c8b18a5e6d93e4a" |
There was a problem hiding this comment.
Can you add a link to a dedicated Singularity container?
There was a problem hiding this comment.
I`ll add that, thanks.
There was a problem hiding this comment.
and I realized I accidentally pushed some branches (pr-extractchannel, pr-register, pr-transformsegmask) to this repository (nf-core/modules). Could these be safely removed? This won’t affect the PR itself. Thanks a lot!
tckumarasekara
force-pushed
the
pr-extractchannel
branch
from
2392ac0 to
dcb6c82
Compare
|
Extra branches deleted as requested. |
itrujnara
left a comment
itrujnara
left a comment
There was a problem hiding this comment.
No more issues, good to go!
3 participants
This PR adds,
stainwarpy
modules for registration of H&E tissue images with their corresponding multiplexed images and to transform the segmentation masks of one image type to be able to use with the other type.
PR checklist
Closes #9701
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda