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fix merge #272

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Aug 24, 2020
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fix merge #272

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6 changes: 3 additions & 3 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -339,9 +339,9 @@ params.intervals = params.genome && !('annotate' in step) ? params.genomes[param
params.known_indels = params.genome && ('mapping' in step || 'preparerecalibration' in step) ? params.genomes[params.genome].known_indels ?: null : null
params.known_indels_index = params.genome && params.known_indels ? params.genomes[params.genome].known_indels_index ?: null : null
params.mappability = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].mappability ?: null : null
params.snpeff_db = params.genome && 'snpeff' in tools ? params.genomes[params.genome].snpeff_db ?: null : null
params.species = params.genome && 'vep' in tools ? params.genomes[params.genome].species ?: null : null
params.vep_cache_version = params.genome && 'vep' in tools ? params.genomes[params.genome].vep_cache_version ?: null : null
params.snpeff_db = params.genome && ('snpeff' in tools || 'merge' in tools) ? params.genomes[params.genome].snpeff_db ?: null : null
params.species = params.genome && ('vep' in tools || 'merge' in tools) ? params.genomes[params.genome].species ?: null : null
params.vep_cache_version = params.genome && ('vep' in tools || 'merge' in tools) ? params.genomes[params.genome].vep_cache_version ?: null : null

// Initialize channels with files based on params
ch_ac_loci = params.ac_loci && 'ascat' in tools ? Channel.value(file(params.ac_loci)) : "null"
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