required hlahd to be installed in path

ylab-hi · Mar 1, 2024 · 39700e6 · 39700e6
1 parent 7145dc4
commit 39700e6
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diff --git a/config/config.yaml b/config/config.yaml
@@ -86,7 +86,6 @@ hlatyping:
   MHC-II_mode: BOTH # DNA, RNA, or BOTH (if empty alleles have to be specified in custom)
 
   # specific path for class II hlatyping (only required when class: II, or BOTH)
-  hlahd_path: ./hlahd.1.7.0/
   freqdata: ./hlahd_files/freq_data/ 
   split: ./hlahd_files/HLA_gene.split.txt
   dict: ./hlahd_files/dictionary/

diff --git a/workflow/rules/hlatyping.smk b/workflow/rules/hlatyping.smk
@@ -430,7 +430,7 @@ rule hlatyping_mhcII:
   threads: config['threads']
   shell:
     """
-      {params.hlahdpath}/hlahd.sh \
+      hlahd.sh \
           -t {threads} \
           -m 100 \
           -c 0.95 \