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Commit 4a6e9492 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch '12-full.path.genomeLocation' into 'develop'

Resolve "Make param.genomeLocation have full path"

Closes #12

See merge request !14
parents 51737889 dcec356b
3 merge requests!29Develop,!16Develop,!14Resolve "Make param.genomeLocation have full path"
Pipeline #3188 passed with stage
in 24 minutes and 49 seconds
......@@ -9,6 +9,7 @@ params.designFile = "$baseDir/../test_data/design.csv"
params.genome = 'GRCh38-3.0.0'
params.genomes = []
params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
params.genomeLocationFull = params.genomeLocation+params.genome
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = 'three'
......@@ -27,7 +28,7 @@ fastqList = Channel
.map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
.collectFile(name: 'fileList.tsv', newLine: true)
refLocation = Channel
.fromPath(params.genomeLocation+params.genome)
.fromPath(params.genomeLocationFull)
.ifEmpty { exit 1, "referene not found: ${params.genome}" }
expectCells = params.expectCells
forceCells = params.forceCells
......
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