pgx-main from experiment server added

pgx-main/README.md

@@ -12,11 +12,23 @@ git clone https://github.com/SBIMB/StellarPGx.git pgx-main
 ### Prepare main directory
 ```bash
 cp -r pgx-engine-wrapper/* pgx-main/
-mv pgx-main/test3.bed pgx-main/resources/cyp2d6/cyp_hg38/test3.bed
 mkdir pgx-main/pgx_results
 rm pgx-main/data/*
 ```
 
+### Update the Chr definitions in main.nf
+Update all Chr<#> to just <#> in `main.nf` (e.g. Chr1 should be 1). Important are lines 226-230 in `main.nf` for cyp2d6.
+
+```groovy
+    if (params.gene=='cyp2d6') {
+        chrom = "22"
+    	region_a1 = "22:42126000-42137500"
+    	region_a2 = "042126000-042137500"
+    	region_b1 = "22:42126300-42132400"
+    	region_b2 = "042126300-042132400"
+	transcript = "ENST00000645361"
+```
+
 ### Place fasta files into pgx-main directory
 (`hg38.fa`, `hg38.fa.fai`). For example:
 ```bash