Gemma kinshipmatrix #8468
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Gemma kinshipmatrix #8468
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mashehu
reviewed
May 15, 2025
Co-authored-by: Matthias Hörtenhuber <[email protected]>
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It now works with docker and singularity, so think good to go except,, the input test data is on another github repo,,,, is this ok?? |
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Not sure how to fix the remaining errors. |
famosab
requested changes
May 23, 2025
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I think we do not want to introduce changes to this files with a new module PR :)
| tuple val(meta2), path(phenotype) | ||
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| output: | ||
| tuple val(meta), path("output/${meta.id}.out.cXX.txt"), emit: matrix |
| -p $phenotype \\ | ||
| -gk \\ | ||
| -o ${meta.id}.out | ||
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Suggested change
| mv output/${prefix}.out.cXX.txt ${prefix}.out.cXX.txt |
| tuple val(meta2), path(phenotype) | ||
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| output: | ||
| tuple val(meta), path("output/${meta.id}.out.cXX.txt"), emit: matrix |
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| tuple val(meta), path("output/${meta.id}.out.cXX.txt"), emit: matrix | |
| tuple val(meta), path("*.out.cXX.txt"), emit: matrix |
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| mkdir output | ||
| touch output/${meta.id}.out.cXX.txt |
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| mkdir output | |
| touch output/${meta.id}.out.cXX.txt | |
| touch ${prefix}.out.cXX.txt |
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| file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.geno.txt.gz", checkIfExists: true) | ||
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| ] | ||
| input[1] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file( "https://raw.githubusercontent.com/genetics-statistics/GEMMA/master/example/mouse_hs1940.pheno.txt", checkIfExists: true), |
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Can you bring those to the test-datasets repository? Or check if there is suitable test-data over there?
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PR checklist
Closes #8463 #8463
This module does the kinship matrix part of gemma.
I cannot get docker to work even though there is a biocontainer, and have not tested with singularity.
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda