I don't konw how to set --variants parameter, and what's wrong with the following code:
nextflow run main.nf --reads '/home/liukai/postd/msi_project/RNAseq1101/00.CleanData/C15*RNA{1,2}.clean.fq.gz' --denylist ~/db/human_genome_index/hg38/S1667195179_agilent_region.hg38.bed —variants /home/liukai/db/human_genome_inde
x/hg38/hg38_VCF/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --results my_msi_results_newref --genome /home/liukai/db/human_genome_index/hg38/hg38_VCF/Homo_sapiens_assembly38.fasta -profile docker -resume
I don't konw how to set --variants parameter, and what's wrong with the following code: nextflow run main.nf --reads '/home/liukai/postd/msi_project/RNAseq1101/00.CleanData/C15*RNA{1,2}.clean.fq.gz' --denylist ~/db/human_genome_index/hg38/S1667195179_agilent_region.hg38.bed —variants /home/liukai/db/human_genome_inde x/hg38/hg38_VCF/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --results my_msi_results_newref --genome /home/liukai/db/human_genome_index/hg38/hg38_VCF/Homo_sapiens_assembly38.fasta -profile docker -resume