Problem 1

Solution

/*
 *  Parse the input parameters
 */

genome_file     =  file(params.genome) (1)
variants_file   =  file(params.variants) (1)
blacklist_file  =  file(params.blacklist) (1)
reads_ch        =  Channel.fromFilePairs(params.reads) (2)
GATK            =  params.gatk (3)

1	Specifiy file objects/file handles using `file()`.
2	Create a channel using fromFilePairs().
3	A basic Nextflow variable can be simply defined.