nf-core
New module: scsplit/count
Summary of changes
New module scsplit/count to demultiplex single-cell data.
PR checklist
Closes #5348
- [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 module conventions in the contribution docs
- [x] If necessary, include test data in your PR.
- [x] Remove all TODO statements.
- [x] Emit the
versions.ymlfile. - [x] Follow the naming conventions.
- [x] Follow the parameters requirements.
- [x] Follow the input/output options guidelines.
- [x] Add a resource
label - [ ] Use BioConda and BioContainers if possible to fulfil software requirements. --> neither docker or conda biocontainer work for scsplit
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- For modules:
- [x]
nf-core modules test <MODULE> --profile docker - [ ]
nf-core modules test <MODULE> --profile singularity - [ ]
nf-core modules test <MODULE> --profile conda
- [x]
- For modules:
Ideally the scsplit tool is put into bioconda, which would make the docker and singularity containers automatically. That would mean that scsplit would be present in the $PATH in all three container engines. If you need help putting scsplit into bioconda, there is a bioconda channel on the nf-core slack.
uld make the docker and singularity containers automatically. That would mean that scsplit would be present in the $PATH in all three container engines. If you need help putting scsplit into bioconda, there is a bioconda channel on the nf-core slack.
scsplit is already available on bioconda(https://anaconda.org/bioconda/scsplit) but idk why it is still not present in $PATH
uld make the docker and singularity containers automatically. That would mean that scsplit would be present in the $PATH in all three container engines. If you need help putting scsplit into bioconda, there is a bioconda channel on the nf-core slack.
scsplit is already available on bioconda(https://anaconda.org/bioconda/scsplit) but idk why it is still not present in $PATH
Well, this PR is currently not using bioconda or the associated biocontainer, so maybe if it is swapped to those it'll work fine?
uld make the docker and singularity containers automatically. That would mean that scsplit would be present in the $PATH in all three container engines. If you need help putting scsplit into bioconda, there is a bioconda channel on the nf-core slack.
scsplit is already available on bioconda(https://anaconda.org/bioconda/scsplit) but idk why it is still not present in $PATH
Well, this PR is currently not using bioconda or the associated biocontainer, so maybe if it is swapped to those it'll work fine?
nope scSplit is still not found in $PATH..
Gernal update:
- I modified the dockerfile because another two functions of scsplit doesnt support newer version of packages like numpy. etc I downgraded to python3.9.
- to make scsplit work in conda, I have opened a PR to add an entry point in the conda package. I tried to provide a solution to call scsplit with command line in conda env before this is merged.
