diff --git a/src/bolero.nf b/src/bolero.nf index e11c46d1a5f6fee49d5c7039143e70887a3aa314..5ea7b7d110ab4af7afbb230126cb68962463a068 100755 --- a/src/bolero.nf +++ b/src/bolero.nf @@ -31,8 +31,8 @@ def helpMessage() { Mandatory arguments: --input [path] Path to the folder containing fast5 files. If skip basecalling option enabled, path to fastq files folder. - --adapt [file] Path to the txt/fasta file containing the sequence of 5'RACE adapter. - --gsp [file] Path to the txt/fasta file containing the sequence of gene-specific primer used in 5'RACE amplification step. + --adapt [file] Sequence of 5'RACE adapter. + --gsp [file] Sequence of gene-specific primer used in 5'RACE amplification step. References: --genome [file] Path to the fasta file containing the genome. @@ -83,7 +83,7 @@ if (params.help || params.h) { params.skipBC = true params.gpu_mode = false params.adapt = "CGACTGGAGCACGAGGACACTGACATGGACTGAAGGAGTAGAAA" -params.gsp = "CGACTGGAGCACGAGGACACTGA" // "TTAGGCAGAGGTGAAAAAGTTG" +params.gsp = "GTGCACACGGTCCGGCAGATG" // "TTAGGCAGAGGTGAAAAAGTTG" // "CGACTGGAGCACGAGGACACTGA" // params.transcriptome = "./data/202201_Full-length_HBV_GTFv3/20220112_preCore_FL_HBV_XGR_transcripts.fasta" params.genome = "/home/xavier/Data/Genome/202201_Full-length_HBV_GTFv3/20230516_HBV_FL_preCore_reference.fasta" params.gtf = "/home/xavier/Data/Genome/202201_Full-length_HBV_GTFv3/20230516_GTF_preCore_FL_HBV_XGR.gtf"