avoid sending hpalofgrep files while testing

Former-commit-id: c3353cf
juanjo255 · Oct 25, 2024 · 5fdbabc · 5fdbabc
1 parent 51aff9c
commit 5fdbabc
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Showing 7 changed files with 5 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,3 +12,4 @@ notes/Internship
 *.tmp
 test/reads/
 mitnanex_rs/target/
+haplogrep*
diff --git a/haplogrep3.jar b/haplogrep3.jar
diff --git a/haplogrep3.jar.REMOVED.git-id b/haplogrep3.jar.REMOVED.git-id
diff --git a/haplogrep_LICENSE b/haplogrep_LICENSE
diff --git a/mitnanex_reference.sh b/mitnanex_reference.sh
@@ -380,7 +380,8 @@ pipe_exec(){
                 filter_by_quality
             fi
             #map_reads
-            variant_calling
+            #variant_calling
+            haplogroup_class
 
         else
             echo "[${color_red}ERROR${no_color}] $?: Something wrong with reference genome."

diff --git a/refseqMT/chrMT.dict b/refseqMT/chrMT.dict
diff --git a/requirements.txt b/requirements.txt
@@ -18,4 +18,5 @@ gatk is better to install a binary release due to license.
 wget https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip
 unzip gatk-4.6.0.0.zip
 wget https://github.com/genepi/haplogrep3/releases/download/v3.2.1/haplogrep3-3.2.1-linux.zip
-unzip haplogrep3-3.2.1-linux.zip
+unzip haplogrep3-3.2.1-linux.zip
+chmod +x haplogrep3.yaml