Commit 6ef511b7 authored by peguerin's avatar peguerin
Browse files

readme update

parent 81cea2e2
......@@ -18,7 +18,7 @@ git clone https://github.com/Grelot/seaConnect--dDocent.git
* [snakemake](https://snakemake.bitbucket.io)
## Dependencies
You will need to have the following programs installed on your computer. Alternatively we provide a singularity container (see below).
You will need to have the following programs installed on your computer. Alternatively we provide a singularity container (see [Singularity](#singularity) section below).
- OSX or GNU Linux
- bash 4.4.19
......@@ -83,11 +83,11 @@ We provide a complete workflow to perform preprocessing of sequencing ngs raw da
* `{sample}` : any sample
### Container
The container (see [Singularity](#singularity) section below) must be stored into the main directory of this project [seaConnect--dDocent](.) with the name `seaconnect.simg`
The container (see [Singularity](#singularity) section above) must be stored into the main directory of this project [seaConnect--dDocent](.) with the name `seaconnect.simg`
### cleaned fastq data
Write the absolute path of the folder containing filtered data after [preprocessing](#-preprocessing) into [config.yaml](01-infos/config_mullus.yaml) `fastq` section `folder` subsection. Prefix of each fastq file you want to process must be write as a list into subsection `file`
Write the absolute path of the folder containing filtered data after preprocessing into [config.yaml](01-infos/config_mullus.yaml) `fastq` section `folder` subsection. Prefix of each fastq file you want to process must be write as a list into subsection `file`
**For instance :**
......
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