diff --git a/illumina/test.nf b/illumina/test.nf index 26d557d..6c579c3 100644 --- a/illumina/test.nf +++ b/illumina/test.nf @@ -5,25 +5,24 @@ nextflow.enable.dsl = 2 workflow { println "\n IDAT to VCF: TEST" println "" - println " IDAT DIR = ${params.idat_dir}" - println " BPM MANIFEST = ${params.manifest_bpm}" - println " CSV MANIFEST = ${params.manifest_csv}" - println " CLUSTER FILE = ${params.cluster_file}" - println " BUILD VERSION = ${params.build_ver}" + println "idat_dir = ${params.idat_dir}" + println "manifest_bpm = ${params.manifest_bpm}" + println "manifest_csv = ${params.manifest_csv}" + println "cluster_file = ${params.cluster_file}" if(params.build_ver == 'hg19') { - println " REFERENCE = ${params.fasta_ref}" + println "fasta_ref = ${params.fasta_ref}" } else { - println " REFERENCE = ${params.fasta_ref}" - println "BAM ALIGNMENT = ${params.bam_alignment}" + println "fasta_ref = ${params.fasta_ref}" + println "bam_alignment = ${params.bam_alignment}" } - println " OUTPUT PREFIX = ${params.output_prefix}" - println " OUTPUT DIR = ${params.output_dir}" - println "ACCOUNT/PROJECT = ${params.account}" - println "QUEUE/PARTITION = ${params.partition}" - println " CONTAINERS DIR = ${params.containers_dir}" + println "output_prefix = ${params.output_prefix}" + println "output_dir = ${params.output_dir}" + println "account = ${params.account}" + println "partition = ${params.partition}" + println "containers_dir = ${params.containers_dir}" println "" //call_genotypes()