Merge a3a94a4 into 23de91e

broadinstitute · Mar 20, 2020 · 76ca57f · 76ca57f
2 parents 23de91e + a3a94a4
commit 76ca57f
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/pipes/WDL/workflows/tasks/tasks_assembly.wdl b/pipes/WDL/workflows/tasks/tasks_assembly.wdl
@@ -269,7 +269,7 @@ task refine_2x_and_plot {
         if [[ ${gatk_jar} == *.tar.bz2 ]]; then
           tar -xjvof ${gatk_jar} -C gatk
           # find the jar and move it one level up if it is buried in a subdir
-          find gatk -mindepth 1 -type f -iname '*.jar' | xargs -I__ mv -f "__" gatk/
+          find gatk -mindepth 2 -type f -iname '*.jar' | xargs -I__ mv -f "__" gatk/
         else
           ln -s ${gatk_jar} gatk/GenomeAnalysisTK.jar
         fi

diff --git a/tools/gatk.py b/tools/gatk.py
@@ -15,6 +15,7 @@
 import logging
 import os
 import os.path
+import re
 import subprocess
 import tempfile
 
@@ -76,6 +77,11 @@ def version(self):
             self._get_tool_version()
         return self.tool_version
 
+    def version_tuple(self):
+        version_match = re.match(r'(\d+)\.(\d+)', self.version())
+        util.misc.chk(version_match, 'Cannot parse GATK version: {}'.format(self.version()))
+        return tuple(map(int, version_match.groups()))
+
     def _get_tool_version(self):
         if self.install_and_get_path().endswith(".jar"):
             cmd = [
@@ -87,7 +93,8 @@ def _get_tool_version(self):
                 self.install_and_get_path(), '--version'
             ]
 
-        self.tool_version = util.misc.run_and_print(cmd, buffered=False, silent=True).stdout.decode("utf-8").strip()
+        self.tool_version = util.misc.run_and_print(cmd, buffered=False, silent=True,
+                                                    stderr=subprocess.DEVNULL).stdout.decode("utf-8").strip()
 
     def ug(self, inBam, refFasta, outVcf, options=None, JVMmemory=None, threads=None):
         options = options or ["--min_base_quality_score", 15, "-ploidy", 4]
@@ -105,7 +112,7 @@ def ug(self, inBam, refFasta, outVcf, options=None, JVMmemory=None, threads=None
             '--num_threads', threads,
             '-A', 'AlleleBalance',
         ]
-        if TOOL_VERSION_TUPLE < (3, 7):
+        if self.version_tuple() < (3, 7):
             opts += ['-stand_call_conf', 0, '-stand_emit_conf', 0]  # deprecated in 3.7+
 
         self.execute('UnifiedGenotyper', opts + options, JVMmemory=JVMmemory)