Collate pangolin output

[pbiology]

What needs to be done: Collect and concatenate the output from Pangolin. Right now all resultfiles from Pangolin lands in the top folder of the output directory. There is also a single file per sample being generated. These should be gathered in a new place and then concatenated together to have a single easy to access output.

Suggestions on how to get it done:

• Create a specific output folder for pangolin files
• Concatenate all files together
• Modify the output from pangolin so the headers correspond to some specified output, perhaps this should be modelled on the FOHm directives for what they should look like.
• This could be part of the collate step

What are the arguments for getting it done:

• Cleaner output and easier to directly process them further in things like upload to various external partners such as FOHM.

[pbiology]

Perhaps this is solved now? What do you think @JD2112 ?

[JD2112]

Perhaps this is solved now? What do you think @JD2112 ?

Yes, I think it's done! Sorry for late reply :)