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Overall looks good, just smallish things here and there!
modules/nf-core/treerecs/main.nf
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| 'biocontainers/treerecs:1.2--h9f5acd7_3' }" | ||
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| input: | ||
| tuple val(meta), path(species_tree), path(gene_trees) |
modules/nf-core/treerecs/main.nf
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| output: | ||
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| tuple val(meta), path("*.nwk"), emit: corrected_trees |
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The tool can produce multiple formats, these need to be supported: https://project.inria.fr/treerecs/treerecs-options/ (see -O). 1
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@jfy133 Hi James, thanks for the comments! for this section, since user is able to specify output format, should these have "optional:true" and skip the "touch" on lines 40 on? I
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| """ | ||
| echo $args | ||
| touch ${prefix}.nwk |
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When adding support for the other output files, make sure to include them here
| id:'test' ] | ||
| - species_tree: | ||
| type: file | ||
| description: Species tree file |
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Please indicate if mandaotry or optional: https://docs-v2--nf-core-docs.netlify.app/docs/specifications/components/modules/documentation#indication-of-input-channel-requirement
| file('https://gitlab.inria.fr/Phylophile/Treerecs/-/raw/master/examples/polytomy_example/speciesTree.txt?ref_type=heads', checkIfExists: true), | ||
| file('https://gitlab.inria.fr/Phylophile/Treerecs/-/raw/master/examples/polytomy_example/geneTree.txt?ref_type=heads', checkIfExists: true), |
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These neeed to be copied over to nf-core/testdatasets, so we can keep 'control' over them and are not deleted by or moved by someone else 1
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| then { | ||
| assert process.success | ||
| assert process.out.corrected_trees.size() == 1 |
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Is there no string you can check inside?
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file('https://gitlab.inria.fr/Phylophile/Treerecs/-/raw/master/examples/polytomy_example/speciesTree.txt?ref_type=heads', checkIfExists: true), |
| [ | ||
| "TREERECS", | ||
| "treerecs", | ||
| "Treerecs (1.2), Inria - Beagle\nTreerecs 1.2" |
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This looks partially faulty, we really only want the number 1
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| } | ||
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| then { | ||
| assert process.success |
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Please wrap all of these 3 inside the same assertAll() 1. You can use other modules as examples
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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PR for the first time.
PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-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