MetaSnk is a modularized Snakemake workflow for the analysis of metagenomic datasets from human microbiomes.
MetaSnk is a reproducible and scalable modularized Snakemake workflow for the analysis of metagenomic datasets from human microbiomes.
MetaSnk wraps system and software dependencies within Singularity containers.
### Modules:
-[rawQC](README_rawQC.md)
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Notice that you can have multiple paired fastq files per sample, but each SampleID-RUN_LANE combination must be unique.
- sample_metadata.tsv: a tab-delimited table with at least two column fields
```
sampleID SubjectID
```
## Usage
### Simple
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In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
##### Create minimal environment
Some rules will use this environment.
conda env create -f ./envs/MetaSnk.yaml
conda activate MetaSnk
##### Download singularity containers and reference databases
MetaSnk wraps system requirements and software dependencies within singularity containers.
Download these containers by running rule 'pullSIFS' :
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snakemake --profile ./profiles/local buildDBS
##### Create minimal environment
Some rules will use this environment.
conda env create -f ./envs/MetaSnk.yaml
#### Step 2: Configure workflow
Configure the workflow according to your needs via editing the file `config.yaml`.
