Update hamronization/abricate #4851
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| input[1] = '' | ||
| input[2] = '' | ||
| input[3] = '' |
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Couldn't you use the same inputs as the main test? What you have works, I'm just curious why you chose to have them remain different!
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I wondered that too.. but then had same thought, 'true not necessarily needed, nm' 😆
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I didn't have a strong opinion about those, but @ahvigil has (see below comment), so I went for same inputs for stub and normal tests now ;)
| process { | ||
| """ | ||
| input[0] = [ [ id:"test" ],file("dummy.tsv") ] | ||
| input[1] = '' |
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i think input[1] should still be one of the valid format strings. If you look at the snapshot for this stub both tsv and json outputs are empty, and the stub will end up doing an echo ... > test. because the format is an empty string. All of that works in that nothing complains, but doesn't totally test the stub in the way that its meant to be used
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Okay, I changed it to the inputs from the normal test to have it as similar as possible. So far, I used stub tests only for modules with intensive ressource demand (e.g. database downloads or 'out of memory' errors on Github CI checks). But yes, makes sense to keep everything else the same between stub and normal test 👍
| echo "hamronize \\ | ||
| abricate \\ | ||
| ${report} \\ | ||
| $args \\ | ||
| --format ${format} \\ | ||
| --analysis_software_version ${software_version} \\ | ||
| --reference_database_version ${reference_db_version} \\ | ||
| > ${prefix}.${format}" | ||
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| touch ${prefix}.${format} |
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no need to both echo and touch here, I think you can pick one
* abricate --migrate_pytest * Complete nf-test + add stub * Fix linting * Fix linting * Update test names * Update stub test * Stage proper input files for stub tests * Remove `echo <command>` from main.nf
* abricate --migrate_pytest * Complete nf-test + add stub * Fix linting * Fix linting * Update test names * Update stub test * Stage proper input files for stub tests * Remove `echo <command>` from main.nf
PR checklist
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware