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Hi! I noticed a small problem when trying to run GLNexus CLI by passing a manifest.txt with my files.
The help description of glnexus_cli describes using the option to pass the manifest file like this: --list, -l expect given files to contain lists of gVCF filenames, one per line
However, the -l option doesn't seem to work. If you don't include an input vcf in your command, it won't run and will just print the help statement. --list works as intended though.