A draft of a simple module to discuss nf-core
#1
Conversation
- Added new binary files: pbmc_1k.h5, barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz to the anndatautils directory. - Updated the Nextflow test for the anndatautils/toh5ad module to validate the conversion of .h5 files to .h5ad format. - Improved assertions in the test to check for successful process execution and correct output file generation.
…and remove container specification
… add snapshot for output validation
…s for improved reliability
… work directory settings
- Added pbmc_1k.h5 file containing the PBMC 1K dataset. - Included barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files in the raw_feature_bc_matrix directory for the dataset.
…dd new config file for tests
…ta paths to use params for improved flexibility
Claptar
requested review from
BioinfoTongLI,
YinshuiChang,
cakirb,
Copilot and
iaaka
There was a problem hiding this comment.
Pull Request Overview
This PR introduces the new tool module "anndatautils/toh5ad" designed for converting AnnData-compatible files into AnnData objects saved as .h5ad files.
- New meta file defines module metadata
- Module configuration for input/output and authorship is added
Files not reviewed (7)
- modules/sanger/anndatautils/toh5ad/Dockerfile: Language not supported
- modules/sanger/anndatautils/toh5ad/main.nf: Language not supported
- modules/sanger/anndatautils/toh5ad/module.config: Language not supported
- modules/sanger/anndatautils/toh5ad/tests/main.nf.test: Language not supported
- modules/sanger/anndatautils/toh5ad/tests/main.nf.test.snap: Language not supported
- nf-test.config: Language not supported
- tests/configs/nf-test.config: Language not supported
|
I still need to add .zarr file conversion |
There was a problem hiding this comment.
Docker file for this module is already on dockage. I think it would still be good to reference Dockerfile somehow. Either by putting it in the module directory or by leaving a link to dockage in meta.yml or README.md file
| type: string | ||
| description: | | ||
| Sample ID to be used as obs_names in the AnnData object | ||
| - - input: |
There was a problem hiding this comment.
should be a single dash. Otherwise, it means sample_id, input and delimiter are the same level.
Also, maybe it's worth renaming input to be some thing more concrete? What type of data do you have in mind?
There was a problem hiding this comment.
Fix dashes, thank you! Well, input can be either file or directory, so I struggled to come up with better name
| params { | ||
| publish_dir_mode = "copy" | ||
| singularity_pull_docker_container = false | ||
| test_data_base = "${projectDir}/tests/data/" |
There was a problem hiding this comment.
we may need a collective decision on this.
There was a problem hiding this comment.
Agreed. I added this just as a draft to enable testing
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Claptar
changed the title
nf-core
This PR is my attempt to stick to
nf-corebest practices as much as possibleThe following changes were introduced:
anndatautilsfor any modules related toAnnDatamanipulationsanndatautils/toh5admoduletests/datafolder for test datatests/configsfolder for all test related configsnf-test.configfile.zarrfile