In this directory are subdirectories for shotgun metagenomics studies.

Currently, it is assumed that we should run nf-core/taxprofiler, nf-core/mag and nf-core/metatdenovo
ALL THREE for all studies found here. References like 'pipeline' or 'scientific pipeline' below refer
to these three. For studies configured with an accessions.tsv file (as opposed to samplesheets), then
nf-core/fetchngs will also be run and the necessary samplesheets will be generated automatically.
 
Each study/ subdirectory needs:	
	1. EITHER a *_samplesheet.csv file for each pipeline to be run OR an accessions.tsv file.
		(See test_samplesheet_study and test_fetchngs_study for examples)
	2. a *-params.json file for each scientific pipeline to be run, with pipeline specific configuration.
	3. fastq.gz files, for studies using samplesheets.

There is also a file `metagenomics_studies.csv` with two columns `studyName` and `studyPath`.
When you have made your subdirectory for your study and are happy w it, you should add
a row to this csv file. Eventually, modifications to this file trigger an Airflow run for the
associated DAG. For now, trigger it manually in the Airflow GUI.

IMPORTANT NOTES:

  - It is best practice to include full (as opposed to relative) paths where they are needed
  - Example directories exist called test_samplesheet_study and test_fetchngs_study
  - There is a file called processed_studies_provenance.csv. Mostly you should NOT touch this.*

* Possible exception being to remove a study to force it to re-run next time metatdenovo_studies.csv
were touched.