UMICollapse module: Drop external dependencies from UMICollapse module tests #7075
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…e tests (nf-core#7075) * Update the umi-tools dedup tests to use the new test data with UMIs. * Update umicollapse tests to use the new UMI test data. * Switch to nf-bam plugin for output validation. --------- Co-authored-by: Matthias Zepper <[email protected]> Co-authored-by: Jonathan Manning <[email protected]>
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Currently, the UMICollapse module tests run on data that is generated in the test
setup{}with external dependencies (umitools/extract,bwa/index,bwa/mem,samtools/index). While this is no problem here in the modules' repository, those tests will fail on the pipeline level, if the additional modules are not installed.While it may, on the long-term, be useful to devise a CI step detecting and installing missing modules for tests (Leon Rauschning made a neat proposal for this), I have now, due to time contraints, opted to add the required files to the test datasets (test-datasets/1390) and change the tests accordingly (this PR).
I have also updated the
umi-tools deduptests, since they so far used inputs without UMIs.PR checklist
nf-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