Merge branch 'master' into ct-add-bwa-depletion

pipes/WDL/workflows/tasks/metagenomics.wdl

@@ -112,6 +112,7 @@ task krona {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "2 GB"
     cpu: 1
+    dx_instance_type: "mem1_ssd1_x4"
   }
 }
 

pipes/WDL/workflows/tasks/reports.wdl

@@ -111,6 +111,7 @@ task fastqc {
     memory: "2 GB"
     cpu: 1
     docker: "quay.io/broadinstitute/viral-ngs"
+    dx_instance_type: "mem1_ssd1_x4"
   }
 }
 
@@ -142,5 +143,6 @@ task spikein_report {
     memory: "3 GB"
     cpu: 2
     docker: "quay.io/broadinstitute/viral-ngs"
+    dx_instance_type: "mem1_ssd1_x4"
   }
 }

pipes/WDL/workflows/tasks/taxon_filter.wdl

@@ -153,5 +153,6 @@ task merge_one_per_sample {
     memory: "7 GB"
     cpu: 4
     docker: "quay.io/broadinstitute/viral-ngs"
+    dx_instance_type: "mem2_hdd2_x4"
   }
 }

util/file.py

@@ -241,6 +241,11 @@ def extract_tarball(tarfile, out_dir=None, threads=None, compression='auto', pip
         elif compression == 'none':
             decompressor = ['cat']
         untar_cmd = ['tar', '-C', out_dir, '-x']
+        if os.getuid() == 0:
+            # GNU tar behaves differently when run as root vs normal user
+            # we want normal user behavior always
+            if 'GNU' in subprocess.check_output(['tar', '--version']).decode('UTF-8'):
+                untar_cmd.append('--no-same-owner')
         log.debug("cat {} | {} | {}".format(tarfile, ' '.join(decompressor), ' '.join(untar_cmd)))
         with open(os.devnull, 'w') as fnull:
             if tarfile == '-':
@@ -250,9 +255,11 @@ def extract_tarball(tarfile, out_dir=None, threads=None, compression='auto', pip
             decompress_proc = subprocess.Popen(decompressor,
                 stdin=inf, stdout=subprocess.PIPE)
             untar_proc = subprocess.Popen(untar_cmd,
-                stdin=decompress_proc.stdout, stderr=fnull)
+                stdin=decompress_proc.stdout) #, stderr=fnull)
             if untar_proc.wait():
                 raise subprocess.CalledProcessError(untar_proc.returncode, untar_cmd)
+            if decompress_proc.wait():
+                raise subprocess.CalledProcessError(decompress_proc.returncode, decompressor)
             if inf is not None:
                 inf.close()
         log.debug("completed unpacking of {} into {}".format(tarfile, out_dir))