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This was referenced Mar 21, 2026
famosab
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Apr 8, 2026
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Looks good a few comments
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This file should not be needed
| @@ -0,0 +1,55 @@ | |||
| process REGENIE_STEP1 { | |||
| tag "${meta.id}:${meta2.pheno_col}" | |||
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Suggested change
| tag "${meta.id}:${meta2.pheno_col}" | |
| tag "${meta.id}" |
| val(bsize) | ||
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| output: | ||
| tuple val(meta2), path("*_pred.list"), path("*.loco.gz"), emit: predictions |
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| output: | ||
| tuple val(meta2), path("*_pred.list"), path("*.loco.gz"), emit: predictions | ||
| tuple val(meta2), path("*.log"), emit: log |
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| tuple val(meta2), path("*.log"), emit: log | |
| tuple val(meta), path("*.log"), emit: log |
| def genotype_flag = plink_genotype_file.name.endsWith('.pgen') ? '--pgen' : '--bed' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def bsize_arg = bsize ?: 1000 | ||
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| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}_pred.list | ||
| printf '' | gzip > ${prefix}_1.loco.gz |
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| printf '' | gzip > ${prefix}_1.loco.gz | |
| echo | gzip > ${prefix}_1.loco.gz |
| output: | ||
| tuple val(meta2), path("*_pred.list"), path("*.loco.gz"), emit: predictions | ||
| tuple val(meta2), path("*.log"), emit: log | ||
| tuple val("${task.process}"), val('regenie'), eval("regenie --version 2>&1 | head -n 1"), topic: versions, emit: versions_regenie |
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| tuple val("${task.process}"), val('regenie'), eval("regenie --version 2>&1 | head -n 1"), topic: versions, emit: versions_regenie | |
| tuple val("${task.process}"), val('regenie'), eval("regenie --version | head -n 1"), topic: versions, emit: versions_regenie |
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and please update the statement so only the bare version ends up in the output
in this case 4.1.2
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This PR adds the
regenie/step1module, which runs REGENIE Step 1 whole-genome regression to fit LOCO ridge models for downstream association testing workflows.Merge dependencies: none. This PR is self-contained and does not require any other split REGENIE PR to merge first.
PR checklist
topic: versions- See version_topicslabelnf-core modules test regenie/step1 --profile dockernf-core modules test regenie/step1 --profile singularitynf-core modules test regenie/step1 --profile conda