New module: fastme #4920
New module: fastme #4920
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modules/nf-core/fastme/main.nf
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| input: | ||
| path infile | ||
| path topo |
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Thinks this is referring to an initial tree topology to use? Might be nice to give it a more descriptive name, something like initial_tree or the likes.
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| output: | ||
| path "*.nwk" , emit: nwk | ||
| path "*_stat.txt" , emit: stats |
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I think it would be good to add optional output channels at least for the more commonly used optional outputs, in particular the bootstrap supports.
modules/nf-core/fastme/meta.yml
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| keywords: | ||
| - phylogenetics | ||
| - newick | ||
| - minimum evolution |
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I think keywords should have no spaces, could just be replaced with an underscore.
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| } | ||
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| test("setoxin - phylip - with_optional_output") { |
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Just a small thing, I would rename this to bootstrap since that is what it's testing
| { assert snapshot(process.out.nwk) }, | ||
| { assert snapshot(process.out.matrix) }, | ||
| { assert snapshot(process.out.bootstrap) } |
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As I understand, the bootstrap result is not deterministic so should not be snapshotted, and without calling .match() it shouldn't even generate a snapshot I don't think.
I suggest just checking for the files manually, or snapshot-matching the list of files in the output dir.
| - matrix: | ||
| type: file | ||
| description: Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten | ||
| pattern: "*.matrix.phy" | ||
| - bootstrap: | ||
| type: file | ||
| description: A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten | ||
| pattern: "*.bootstrap" |
modules/nf-core/fastme/main.nf
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| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: infile | ||
| """ | ||
| touch ${prefix}.nwk | ||
| touch ${prefix}_stat.txt |
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As a pipeline may rely on the optional output of -B, the stub should also generate these if the argument is passed.
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Looks good, merging! |
* Added main, started creating tests * Fixed tests * Fixed tests again * Fixed tests, completed meta.yml * Minor lint issue fix * Fix typo * Renamed initial tree argument, added optional outputs and the associated test * Removed a space in meta.yml * Added optional outputs to stub, changed bootstrap test --------- Co-authored-by: Leon Rauschning <[email protected]>
* Added main, started creating tests * Fixed tests * Fixed tests again * Fixed tests, completed meta.yml * Minor lint issue fix * Fix typo * Renamed initial tree argument, added optional outputs and the associated test * Removed a space in meta.yml * Added optional outputs to stub, changed bootstrap test --------- Co-authored-by: Leon Rauschning <[email protected]>
PR checklist
Closes #4889
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-awareNote: Conda test was not run locally due to a conda issue seemingly independent of the module (exit code 143, terminated by the system).