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decontamination workflow #72

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decontamination workflow #72

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LaurenHuet
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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
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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

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@LaurenHuet