New module: SKA/DISTANCE #7437
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New module: SKA/DISTANCE #7437
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Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>
Co-authored-by: Sateesh_Peri <[email protected]>
famosab
reviewed
Feb 6, 2025
modules/nf-core/ska/distance/main.nf
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| """ | ||
| touch ${prefix}.distances.tsv | ||
| touch ${prefix}.clusters.tsv | ||
| touch ${prefix}.cluster.1.txt |
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Can you adjust this stub test to produce a different number of cluster.*.txt files based on the args or the input?
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The number of clusters is not determinable from the size of the input, but I can assume every input file is a separate cluster
modules/nf-core/ska/distance/main.nf
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| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.distances.tsv | ||
| touch ${prefix}.clusters.tsv | ||
| touch ${prefix}.cluster.1.txt | ||
| touch ${prefix}.dot |
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More general: Can the stub be modified so that only the files are produced that are to be expected upon a specific input (because you marked the outputs as optional)?
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>
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Implementing the list test took way too long, but it works now. I hope I haven't added too many evil lines. |
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PR checklist
Add SKA/DISTANCE module
There is no non-stub test for the list input because SKA cannot handle URLs in the list
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda