Calculate output file md5 hashes and file sizes.

[ajmaurais]

How the hash file is generated

• A tsv file is created at the end of the workflow with output file names, paths, md5 hashes, and the file size in bytes.
• The file sizes and hashes are calculated of all outputs during DiaNN and EncyclopeDIA searches and written to a text file.
• The hash of the final skyline.zip file is written to a file during the Skyline merge or annotate step
• The hash txt files are processed and merged into a channel by a new combine_file_hashes sub-workflow.
• The hashes of additional output files are calculated by a separate process during the combine_file_hashes workflow

Under the hood changes

• Move container_images.config to conf
• Define paths used in process publishDir directives to conf/output_directories.config. The output file paths are read by each process and by the combine_file_hashes workflow so that the paths can be included in the hash file.