diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 2f8a87d7..b20e3926 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,4 +1,4 @@ sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed,vardict_min_af NA24143,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24143.cram,,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/genome/test.ped,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz.tbi,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01 NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24149.vcf.gz,,, -NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, +NA24385,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, diff --git a/main.nf b/main.nf index 0ca8b4c1..285e1280 100644 --- a/main.nf +++ b/main.nf @@ -177,7 +177,7 @@ workflow { } } - callers = params.callers.tokenize(",") + def callers = params.callers.tokenize(",") callers.each { caller -> if(!(caller in GlobalVariables.availableCallers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${GlobalVariables.availableCallers}")} } @@ -194,10 +194,6 @@ workflow { def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" -<<<<<<< HEAD - print(params.genomes) -======= ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 // // SUBWORKFLOW: Run initialisation tasks //