umitools/extract and umitools/dedup are saving extra copies of input files

[anoronh4]

In practice, these two modules are saving extra copies of the input files because of the following nextflow bug: nextflow-io/nextflow#3995

The output channels do not actually contain the input files when the process is complete because by default symlinks are excluded. however, for whatever reason when you are using the scratch directive, all files are copied over regardless of whether they are symlinks or not, which leads to the input files being saved as a hard link, not a soft-link. this leads to unnecessary storage usage, especially because the new file is not a hard link pointing to the original source of the file, but an actual copy with a different inode.

until nextflow fixes this bug we need to make sure the output declaration doesn't match the input files, especially when the inputs are quite large.