diff --git a/workflow/main.nf b/workflow/main.nf index 4072b260ac29218dc2a0ea146f6f61b34053a688..9ed1726ebe07387cf8395a1057e4506633c6dcdf 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -12,6 +12,7 @@ params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: f params.expectCells = 10000 params.forceCells = 0 params.version = '3.0.2' +params.outDir = "$baseDir/output" // Define regular variables designLocation = Channel @@ -28,10 +29,11 @@ refLocation = Channel expectCells = params.expectCells forceCells = params.forceCells version = params.version +outDir = params.outDir process checkDesignFile { - publishDir "$baseDir/output", mode: 'copy' + publishDir "$outDir/${task.process}", mode: 'copy' input: @@ -78,7 +80,7 @@ forceCells302 = forceCells process count211 { tag "count211-$sample" - publishDir "$baseDir/output", mode: 'copy' + publishDir "$outDir/${task.process}", mode: 'copy' input: @@ -109,7 +111,7 @@ process count211 { process count301 { tag "count301-$sample" - publishDir "$baseDir/output", mode: 'copy' + publishDir "$outDir/${task.process}", mode: 'copy' input: @@ -140,7 +142,7 @@ process count301 { process count302 { tag "count302-$sample" - publishDir "$baseDir/output", mode: 'copy' + publishDir "$outDir/${task.process}", mode: 'copy' input: