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- 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
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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
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I still need to add .zarr file conversion |
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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: |
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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?
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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/" |
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we may need a collective decision on this.
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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
2 participants
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