Merge branch 'master' into 'public'

merge master into public See merge request icbi-lab/pipelines/rnaseq-nf!40
icbi-lab · Aug 3, 2022 · 8ac296d · 8ac296d
2 parents dbba4df + 09d2f0c
commit 8ac296d
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diff --git 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:

diff --git a/nextNEOpi.nf b/nextNEOpi.nf
@@ -5433,13 +5433,15 @@ 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
         bash -c "./configure"
         cd /opt/iedb/
         rm -f $mhci_file
 
+        rm -f $mhcii_file
         wget $iedb_MHCII_url
         tar -xzvf $mhcii_file
         cd mhc_ii