stub and nf-test created for raxmlng #8161
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I know you are just swapping to nf-test, but think this module could do with some improvements.
I think this module should have a meta map. Then we can use meta.id as the default prefix, as normal.
Is the --model a required argument? As then it should be an input channel; please don't define extra task.ext.foo values.
Can you make the optional file in the stub (bonus points if you make it conditional on something being passed to args, if that is how it decides to make it.
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If you are not comfortable adjusting the module, I can do that for you. |
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Oh, and don't forget to remove the pytest files and the entry from the pytest config file. |
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And while you are there, you can remove the pytest files and entry for |
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@SPPearce
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You can use a modules_args parameter to pass the bootstrapping option to the args, to test that directly rather than adding a new extra parameter.
See https://github.com/nf-core/modules/blob/c9c3ef86c1892413b3c86fb38c4e39fd7288512f/modules/nf-core/ataqv/ataqv/tests/main.nf.test for instance.
| tuple val(meta), path("*.raxml.bestTree") , emit: phylogeny | ||
| tuple val(meta), path("*.raxml.support"), optional:true, emit: phylogeny_bootstrapped | ||
| path "versions.yml" , emit: versions |
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Can you put the emit: first, then the optional:, so it lines up better.
| type: map | ||
| description: Groovy Map containing sample information |
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This should still be the previous description and type:
| - "*.raxml.support": | ||
| type: file | ||
| description: A phylogeny in Newick format with bootstrap values | ||
| type: map |
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This should still be the previous description and type
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| raxmlng: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//') | ||
| END_VERSIONS | ||
| """ | ||
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| stub: | ||
| def args = task.ext.args ?: params.raxmlng_args ?: '' |
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| def args = task.ext.args ?: params.raxmlng_args ?: '' | |
| def args = task.ext.args ?: '' |
| if (!meta.id) { | ||
| error "Input meta map does not contain 'id'. Received: ${meta}" | ||
| } | ||
| // Use a dedicated param for stub testing the bootstrap output scenario |
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| if (!meta.id) { | |
| error "Input meta map does not contain 'id'. Received: ${meta}" | |
| } | |
| // Use a dedicated param for stub testing the bootstrap output scenario |
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| stub: | ||
| def args = task.ext.args ?: params.raxmlng_args ?: '' | ||
| def prefix = task.ext.prefix ?: meta.id |
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| def prefix = task.ext.prefix ?: meta.id | |
| def prefix = task.ext.prefix ?: "${meta.id}" |
PR checklist
Closes #7676
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