decontamination workflow

[LaurenHuet]

added sub workflow for decontamination pipeline, write 2 local modules, (these still contain some // comments for NF-CORE to do. Could possibly make one of these into an actual NF-core module.

Fixed issues with the decompression of gzipped files

[LaurenHuet]

Actions:
need to update sample sheet to include taxon id (NCBI taxon ID for fcs to run properly) this then needs to be updated in the workflow, currently just being passed into the process as a value.
Need documentation for how to install NCBI db locally which can be passed onto the command line

[FernandoDuarteF]

Hi @LaurenHuet, are you going to continue with this PR?

If not, is it OK if I carry on from here? Using your fork.

[LaurenHuet]

Hi Fernando,
I had stopped working on it as @mahesh-panchal was making some changes to the fcsgx modules, I'm not certain if all the updates he wanted to make are complete as of yet?

[mahesh-panchal]

I've been a bit busy. There's still the fcs adapter modules to update, but to be honest, don't let my non-progress stop you. Incorporate what's been done already and complete the PR. You can always make a new PR later to update the modules once they're updated on nf-core.

[FernandoDuarteF]

Hi @LaurenHuet.

I think merging this should be straight forward except for the conflicts that have to be resolved. The pipeleline has changed a bit in the last few weeks, you might have some problems resolving conflicts. Is it okay if I do it for you?