Hifiadapterfilt #7398
Hifiadapterfilt #7398
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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 <[email protected]>
Co-authored-by: Evangelos Karatzas <[email protected]>
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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: |
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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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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