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refactor: add check for terra parms CDCgov#151
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slsevilla committed Apr 1, 2024
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Expand Up @@ -44,6 +44,7 @@ workflow PHOENIX {
def checkPathParamList = [ params.input, params.multiqc_config, params.kraken2db] //removed , params.fasta to stop issue w/connecting to aws and igenomes not used
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
if (params.ica != true && params.ica != false) {exit 1, "Please set params.ica to either \"true\" if running on ICA or \"false\" for all other methods."}
if (params.terra != true && params.terra != false) {exit 1, "Please set params.terra to either \"true\" if running on terra or \"false\" for all other methods."}

//input on command line
if (params.input) { ch_input = file(params.input) } else { exit 1, 'For -entry PHOENIX: Input samplesheet not specified!' }
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