usage/reference.md

@@ -87,15 +87,16 @@ The help can be visualized with:
 
 ```
 $ python SCRIPTS/make_ref.py -h
-usage: make_ref.py [-h] [-p {refseq,gencode,ensembl}] [-s {human,mouse,rat}]
-                   [-r DIR] [-n REFNAME] [-u PROXY]
+usage: make_ref.py [-h] [-p {refseq,gencode,ensembl}]
+                   [-s {human,mouse,rat,cow,chicken}] [-r DIR] [-n REFNAME]
+                   [-u] [--ensemblRelease ENSRELEASE]
 
 optional arguments:
   -h, --help            show this help message and exit
   -p {refseq,gencode,ensembl}, --provenance {refseq,gencode,ensembl}
                         Provenance of the reference transcriptome to be
                         downloaded (default : refseq).
-  -s {human,mouse,rat,cow}, --species {human,mouse,rat,cow}
+  -s {human,mouse,rat,cow,chicken}, --species {human,mouse,rat,cow,chicken}
                         Species of the reference transcriptome to be
                         downloaded (default: human). If you need another
                         species, you're going to have to build your reference
@@ -109,10 +110,12 @@ optional arguments:
   -n REFNAME, --name REFNAME
                         Name of the new reference (default to standard last
                         build name according to chosen species. Ex:
-                        hg38,mm10,rn6,cow). This name should be the same specified
-                        in the samplesheet describing the samples.
-  -u PROXY, --use-proxy PROXY
-                        Use univ-nantes proxy
+                        hg38,mm10,rn6,bosTau9). This name should be the same
+                        specified in the samplesheet describing the samples.
+  -u, --use-proxy       Use univ-nantes proxy
+  --ensemblRelease ENSRELEASE
+                        Specific ensembl release to use. If not specified,
+                        uses last one available.
 ```
 
 Examples: