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In the following pull request I tried to create a new module that converts the
morphology.ome.tiffimage into severalpngimages depending on the amount of resolutions and series present in the originalome.tiff.The module uses bftools by bioformats. The main command used is bfconvert, additional information on how to use the command is here.
Since this was the first time I did any type of contribution to nf-core I did not follow the usual workflow for creating a module and adding it to the pipeline 😅. Therefore there are multiple files/folders missing (such as test.nf and meta.yml). Additionally I was not able to integrate the module into the main spatialxe pipeline.
I did test the module and everything appears to be working as intended!
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).