diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml index 03b65279bf0fb7cdbeeed7575dad4896abd08f15..ccabafa55e254d6b3a8c7776b6b939141285d4fa 100755 --- a/astrocyte_pkg.yml +++ b/astrocyte_pkg.yml @@ -97,15 +97,15 @@ workflow_parameters: - id: genome type: select choices: - - [ '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0', 'Human GRCh38 release 93'] - - [ '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38 release 84'] - - [ '/project/apps_database/cellranger/refdata-cellranger-hg19-3.0.0', 'Human GRCh37 (hg19) release 87'] - - [ '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19) release 84'] - - [ '/project/apps_database/cellranger/refdata-cellranger-mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93'] - - [ '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84'] - - [ '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93'] - - [ '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84'] - - [ '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In'] + - [ 'refdata-cellranger-GRCh38-3.0.0', 'Human GRCh38 release 93'] + - [ 'refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38 release 84'] + - [ 'refdata-cellranger-hg19-3.0.0', 'Human GRCh37 (hg19) release 87'] + - [ 'refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19) release 84'] + - [ 'refdata-cellranger-mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93'] + - [ 'refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84'] + - [ 'refdata-cellranger-hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93'] + - [ 'refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84'] + - [ 'refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In'] required: true description: | Reference species and genome used for alignment and subsequent analysis. diff --git a/workflow/main.nf b/workflow/main.nf index f16d221dfe2dca69cee8a08e5dc99027890744d6..7d634a2a9818847213c6ce0a3a3014c526527d86 100755 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -6,7 +6,7 @@ // Define Input variables params.fastq = "$baseDir/../test_data/*.fastq.gz" params.designFile = "$baseDir/../test_data/design.csv" -params.genome = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0' +params.genome = 'refdata-cellranger-GRCh38-1.2.0' params.expectCells = 10000 params.forceCells = 0 params.version = '3.0.2' @@ -21,7 +21,7 @@ fastqList = Channel .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") } .collectFile(name: 'fileList.tsv', newLine: true) refLocation = Channel - .fromPath(params.genome) + .fromPath('/project/apps_database/cellranger/'+params.genome) .ifEmpty { exit 1, "referene not found: ${params.genome}" } expectCells = params.expectCells forceCells = params.forceCells