From 96d364fd831637de0cb7ec78f779bf80412be0f3 Mon Sep 17 00:00:00 2001
From: Dietmar Rieder <dietmar.rieder@i-med.ac.at>
Date: Wed, 13 Jul 2022 09:46:55 +0200
Subject: [PATCH 1/3] Merge branch 'methylnick-patch-1' into public, closes #9

---
 conf/params.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/params.config b/conf/params.config
index 989e8cd..1eee688 100644
--- a/conf/params.config
+++ b/conf/params.config
@@ -110,7 +110,7 @@ params {
   HLA_HD_genome_version = "hg38"
 
   // URL to the installation package of MIXCRC, will be installed automatically.
-  MIXCR_url       = "https://github.com/milaboratory/mixcr/releases/download/v4.0.0/mixcr.zip"
+  MIXCR_url       = "https://github.com/milaboratory/mixcr/releases/download/v4.0.0/mixcr-4.0.0.zip"
   MIXCR_lic       = "" // path to MiXCR license file
   MIXCR           = "" // Optional: specify path to mixcr directory if already installed, will be installed automatically otherwise
   // analyze TCRs using mixcr

From c729c06f5aa36721dbd4ba0636dc84c74baabbb9 Mon Sep 17 00:00:00 2001
From: Dietmar Rieder <dietmar.rieder@i-med.ac.at>
Date: Mon, 18 Jul 2022 16:45:32 +0200
Subject: [PATCH 2/3] prevent saving iedb files with suffix after failed
 downloads. Closes #36.

---
 nextNEOpi.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nextNEOpi.nf b/nextNEOpi.nf
index b695b2a..8f476b0 100644
--- a/nextNEOpi.nf
+++ b/nextNEOpi.nf
@@ -5433,6 +5433,7 @@ if(!iedb_chck_file.exists() || iedb_chck_file.isEmpty()) {
         """
         CWD=`pwd`
         cd /opt/iedb/
+        rm -f $mhci_file
         wget $iedb_MHCI_url
         tar -xzvf $mhci_file
         cd mhc_i
@@ -5440,6 +5441,7 @@ if(!iedb_chck_file.exists() || iedb_chck_file.isEmpty()) {
         cd /opt/iedb/
         rm -f $mhci_file
 
+        rm -f $mhcii_file
         wget $iedb_MHCII_url
         tar -xzvf $mhcii_file
         cd mhc_ii

From 09d2f0c0e89bc5cd368bedcc61ae43da0745954c Mon Sep 17 00:00:00 2001
From: Dietmar Rieder <dietmar.rieder@i-med.ac.at>
Date: Wed, 3 Aug 2022 10:43:44 +0200
Subject: [PATCH 3/3] fix parser. Key not found when there is no gene SYMBOL in
 vcf record. closes #10

---
 bin/parse_mixMHC2pred.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/bin/parse_mixMHC2pred.py b/bin/parse_mixMHC2pred.py
index 1e72c20..987439c 100755
--- a/bin/parse_mixMHC2pred.py
+++ b/bin/parse_mixMHC2pred.py
@@ -76,6 +76,8 @@ def parse_vcf(vep_vcf, sample_name, normal_name):
         enst = CSQ[6]
         variant = CSQ[14] + CSQ[15]
 
+        gene_symbol = gene_symbol if gene_symbol else ensg
+
         vcf_record = {
             "chrom": chrom,
             "pos": pos,
@@ -94,6 +96,7 @@ def parse_vcf(vep_vcf, sample_name, normal_name):
             "variant": variant,
         }
 
+
         if "frameshift_variant" in variant_type.split("&"):
             key = gene_symbol + "_" + enst + "_" + CSQ[14] + ref + "/" + alt
         else: