error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ref_path: ${ref_path}\nOR ref_file: ${ref_file}\nPARAMETER IN nextflow.config FILE\n\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
}
def file_exists4 = k2db_ch_test.exists()
if( ! file_exists4){
error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID kraken db path: ${kraken_db}\nPARAMETER IN nextflow.config FILE\n\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
if(system_exec == 'slurm'){
def file_exists4 = k2db_ch_test.exists()
if( ! file_exists4){
error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID kraken db path: ${kraken_db}\nPARAMETER IN nextflow.config FILE\n\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
}
}
}else{
error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID system_exec PARAMETER IN nextflow.config FILE: ${system_exec}\n\n========\n\n"
...
...
@@ -161,15 +167,22 @@ process kraken {
input:
file fastq from fastq_trim_ch3
file k2db
if(system_exec == 'slurm'){
file k2db
}
output:
file "${fastq.baseName}_kraken_std.txt" into krakenreports