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Merge pull request #206 from genomic-medicine-sweden/path_params

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Add path parameters
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James A. Fellows Yates 2022-12-23 15:05:59 +01:00 committed by GitHub
commit 2de049399d
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1 changed files with 5 additions and 3 deletions
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workflows/taxprofiler.nf
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@ -11,9 +11,11 @@ WorkflowTaxprofiler.initialise(params, log)
// TODO nf-core: Add all file path parameters for the pipeline to the list below // TODO nf-core: Add all file path parameters for the pipeline to the list below
// Check input path parameters to see if they exist // Check input path parameters to see if they exist
def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference, def checkPathParamList = [ params.input, params.genome, params.databases,
params.shortread_hostremoval_index, params.multiqc_config, params.outdir, params.longread_hostremoval_index
params.shortread_qc_adapterlist params.hostremoval_reference, params.shortread_hostremoval_index,
params.multiqc_config, params.shortread_qc_adapterlist,
params.krona_taxonomy_directory
] ]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }