Add PDC as an input file source

[ajmaurais]

• Important new workflow parameters

  • params.pdc.study_id When this option is set raw files and metadata are downloaded from the PDC using the PDC_client to interface with the PDC.
  • params.pdc.n_raw_files Limit processing to n raw files. This is useful for testing. For now this only applies to when files are downloaded from the PDC. This might be useful as a workflow option that would apply globally.

• Code refactoring

  • raw files are downloaded and converted once at the beginning of main.nf
  • Wide window files can be local, downloaded from Panorama or downloaded from the PDC.
  • Optional narrow window files can be local or downloaded from Panorama.
  • If params.msconvert_only == true the mzML file channel(s) are uploaded to panorama and the workflow exits.
  • Otherwise the mzML files are searched with EncyclopeDIA or DiaNN.