added separate rules for MHC-II prediction tools download

workflow/rules/prioritization.smk

@@ -1,10 +1,10 @@
-rule download_prediction_affinity_tools:
+rule download_mhcI_ba_tools:
   output:
     directory("workflow/scripts/mhc_i/")
   message:
     "Downloading MHC I prediction tools"
   log:
-    "logs/download_prediction_affinity_tools.log"
+    "logs/download_mhc-I_ba_tools.log"
   conda:
     "../envs/basic.yml"
   shell:
@@ -13,6 +13,21 @@ rule download_prediction_affinity_tools:
           | tar xz -C workflow/scripts/
     """
 
+rule download_mhcII_ba_tools:
+  output:
+    directory("workflow/scripts/mhc_ii/")
+  message:
+    "Downloading MHC II prediction tools"
+  log:
+    "logs/download_mhc-II_ba_tools.log"
+  conda:
+    "../envs/basic.yml"
+  shell:
+    """
+      curl -L -o - https://downloads.iedb.org/tools/mhcii/3.1/IEDB_MHC_II-3.1.tar.gz \
+          | tar xz -C workflow/scripts/ > {log} 2>&1
+    """
+
 rule download_prediction_binding_affinity_tools:
   output:
     directory("workflow/scripts/immunogenicity/")
@@ -38,7 +53,8 @@ rule prioritization:
     annotation="resources/refs/genome_tmp.gtf",
     counts="results/{sample}/quantification/allcounts.txt",
     mhcI_ba="workflow/scripts/mhc_i/",
-    mhcI_im="workflow/scripts/immunogenicity/"
+    mhcI_im="workflow/scripts/immunogenicity/",
+    mhcII_ba="workflow/scripts/mhc_ii/"
   output:
     directory("results/{sample}/prioritization/"),
   message: