DOCS: remove absolut path from doc and examples

docs/source/install.md

@@ -12,7 +12,7 @@ $ git clone https://forgemia.inra.fr/umr-gdec/magatt.git
 We recommend to build the environment using conda (developped with miniconda 3, conda 4.9.2 ) with the file [environment.yml](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/envs/environment.yml):  
 
 ```console
-$ conda env create -f environment.yml -n magatt
+$ conda env create -f envs/environment.yml -n magatt
 ```
 
 Once created, you can  activate the environment with:

docs/source/pipeline_conf.md

@@ -31,7 +31,7 @@ Here, we only need the fasta of the new genome assembly
 | Parameter in `config.yaml` | format |description |Example |  
 |----------------------------|--------|------------|--------|  
 |**targetFasta**|FASTA|fasta file of the target genome assembly on which we transfert the annotation|targetFasta: 'data/CS_pesudo_v2.1.fa'|  
-|**targetBwaIdx**|BWA index|Prefix for the BWA index files|targetBwaIdx: '/data/db/triticum_aestivum/arinalrfor/current/bwa/all'|  
+|**targetBwaIdx**|BWA index|Prefix for the BWA index files|targetBwaIdx: '/data/db/triticum_aestivum/julius/current/bwa/all'|  
 |**targetGmapIndex**|PATH|Name of the GMAP index directory. This will be used with the `-d` option of `gmapl`|targetGmapIndex: 'ensembl_Triticum_aestivum_julius_2022-9-16'|  
 |**targetGmapIndexPath**|PATH|Full path to the directory in which the GMAPindex is found. This will be used with the `-D` option of `gmapl`|targetGmapIndexPath: '/data/db/triticum_aestivum/julius/gmapdb/all/'|  
 

docs/source/run_pipeline.md

@@ -32,7 +32,7 @@ $ snakemake -j 32 --cluster sbatch
 
 This will allow to have at most 32 subproccess run through the SLURM scheduler with `sbatch`.
 
-You can use a custom [cluster.json](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/cluster.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:    
+You can use a custom [cluster.json](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/cluster-hpc2.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:    
 
 ```console
 $ snakemake -j 32 --cluster-config cluster-hpc2.json --cluster "sbatch -J {cluster.jobName} -c {cluster.c} --mem {cluster.mem} -e {cluster.error} -o {cluster.output} -p gdec" --verbose"