5127 new module xenium ranger #6826
Conversation
…uite changes,readme update
…ule for xeniumranger rename
…ule for xeniumranger rename
khersameesh24
requested review from
vagkaratzas
and removed request for
a team
…ersameesh24/modules into 5127-new-module-xenium-ranger
…ersameesh24/modules into 5127-new-module-xenium-ranger
5127 new module xenium ranger
| val(meta) | ||
| path(xenium_bundle) | ||
| val(expansion_distance) | ||
| path(coordinate_transform) | ||
| path(nuclei) | ||
| path(cells) | ||
| path(transcript_assignment) | ||
| path(viz_polygons) |
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Sample specific data should go in the same tuple as meta.
Reference data should either go in one tuple with it's own meta or in separate channels per datatype, again each with it's own meta
example: https://github.com/nf-core/modules/blob/master/modules/nf-core/snapaligner/align/main.nf#L10
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Code Changed -> Tested -> Updated PR ✌🏻
| val(meta) | ||
| path(xenium_bundle) | ||
| val(expansion_distance) | ||
| path(coordinate_transform) | ||
| path(nuclei) | ||
| path(cells) | ||
| path(transcript_assignment) | ||
| path(viz_polygons) |
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| path(viz_polygons) | ||
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| output: | ||
| tuple val(meta), path("**/outs/**"), emit: outs |
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What does the tool output? different file formats should also have different output channels
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Hi Matthias, the output for xeniumranger modules is reupdated in the input files just like other 10x tools, multiple files are updated for every run and hence we do not have a dedicated channel for the outputs
PR checklist
Closes #XXX
versions.ymlfile.labelnf-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