Currently, the spot2cell data is reformatted to fit the anndata spatial requirements and then an anndata object is created. In the current version, the columns to remove from spot2cell are hardcoded.
This PR closes the #26.
[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
[x] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/molkart branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[x] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).
PR checklist
This PR adds an additional output format downstream of spot2cell, namely data formatted in the anndata format as described in the squidpy tutorial: https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_read_spatial.html
Currently, the spot2cell data is reformatted to fit the anndata spatial requirements and then an anndata object is created. In the current version, the columns to remove from spot2cell are hardcoded.
This PR closes the #26.
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).