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Looks good! Just some minor comments; I understand that at the moment there is only one pacbio test dataset, that unfortunately doesn't have any adapters to filter. Would it be easy/possible to upload another pacbio minimal test dataset where adapters are getting filtered out (and probably also have fewer to non empty output files)? Also, even though the conda environment and the containers describe version 3.0.0, in the versions.yml, 3.0.1 is written out. Can you investigate why the mismatch?
Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
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The test produces no snaps at all - maybe this can be changed?
| { assert snapshot(process.out[0][1].findAll { | ||
| file(it).name == "test.filt.fastq.gz" && | ||
| file(it).name == "test.contaminant.blastout" && | ||
| file(it).name == "test.blocklist" }).match()}, | ||
| { assert path(process.out.stats[0].get(1)).text.contains('Number of adapter contaminated ccs reads: 0 (0% of total)') }, |
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These files seem to not be found in the snapshot?
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) |
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can you change this to the newer path description? :)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)
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| task.ext.when == null || task.ext.when | ||
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| script: | |
| script: |
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| // The tool AUTOMATICALLY detects fastq files from the input folder, hence an explicit call of "fastq" is not needed. | ||
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Hi @Ge94, |
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Hi @FloWuenne @famosab , thank you for your comments. I paused this PR and its failing tests, as my main issue is finding or creating a meaningful sample to launch this tool on. At the moment, those that I found have no adapters to filter, hence the output is essentially the same as the input. I tried with all hifi files I could find in nf-core/test-datasets, but none suit my case. Do you have any recommendations or documentation I could follow to generate my own sample and add it to the repo? Thank you 😊 |
You can add new test data here: https://github.com/nf-core/test-datasets/blob/modules/README.md |
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Closing due to lack of response. Please reopen if you (or anyone else) have any plans to continue. |
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in 2025 spring cleaning - modules (PRs)
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This PR was created to introduce hifiadapterfilt as a new module. It's purpose is to remove adapters that are specific to pacbio hifi reads.
PR checklist
Closes #7390
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda