UPDATE: add ne gmap management in Readme description

README.md

@@ -81,6 +81,8 @@ 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'|
+|**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: '/home/data/triticum_aestivum/julius/gmapdb/all/'|
 
 * Output parameters/settings
 
@@ -136,6 +138,11 @@ refChrom: ['chr1A', 'chr1B', 'chr1D', 'chr2A', 'chr2B', 'chr2D', 'chr3A', 'chr3B
 
 ##### TARGET related files/parameters (refseqv2.1)
 targetFasta: 'data/CS_pesudo_v2.1.fa'
+#GMAP index of the genome for -d option
+targetGmapIndex: 'ensembl_Triticum_aestivum_julius_2022-9-16'
+#GMAP index: path to the gmapindex directory, for -D option
+targetGmapIndexPath: '/home/herimbert/gdec/shared/triticum_aestivum/julius/current/gmapdb/all/'
+
 
 ##### ISBP/markers related config and parameters
 # BAM file of markers/ISBPs mapped on the target genome (REFSEQ v2.1)