Commit c54b0fc4 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

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### 1. General mandatory files
Launching metagWGS involves the use of mandatory files:
* The **metagenomic whole genome shotgun data** you want to analyze: `.fastq` or `.fastq.gz` R1 and R2 files (Illumina HiSeq3000 or NovaSeq sequencing, 2*150bp).
* The **metagenomic whole genome shotgun data** you want to analyze: `.fastq` or `.fastq.gz` R1 and R2 files (Illumina HiSeq3000 or NovaSeq sequencing, 2*150bp). For a cleaner MultiQC html report at the end of the pipeline, raw data with extension `_R1` and `_R2` are preferred to those with extensions `_1` and `_2`.
* The **metagWGS.sif** and **eggnog_mapper.sif** Singularity images (into `metagwgs/dev` folder).
### 2. Mandatory files for certain steps
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