Merge pull request #23 from dufeiyu/white_space

Remove white spaces from lane, flowcell, index and set dragen-3 as default dragen queue
dhslab · Dec 9, 2024 · 54bee1f · 54bee1f
2 parents cbbdfdb + 24462e2
commit 54bee1f
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Showing 3 changed files with 7 additions and 2 deletions.
diff --git a/Soma.json b/Soma.json
@@ -13,6 +13,6 @@
     "Soma.DragenMEM":"200 G",
     "Soma.DragenEnv":"LSF_DOCKER_DRAGEN=y",
     "Soma.DragenDockerImage":"gtac-mgi-dragen(apldx/oracle8-dragen-4.3.6)",
-    "Soma.DragenQueue":"dragen-2",
+    "Soma.DragenQueue":"dragen-3",
     "Soma.Queue":"gtac-mgi"
 }
diff --git a/scripts/QC_metrics.py b/scripts/QC_metrics.py
@@ -57,6 +57,7 @@ def get_sample_list(directory):
 total_giga_bases= []
 
 for sample_name in sample_list:
+    sample_name = sample_name.replace(" ", "")
     search = os.path.join(out_dir, f"{sample_name}*")
     sample_dir = glob.glob(search)[0]
     if not os.path.isdir(sample_dir):

diff --git a/scripts/launcher.pl b/scripts/launcher.pl
@@ -104,7 +104,11 @@
     }
     my ($lane, $flowcell, $name, $index, $exception) = @$row;
 
-    $name =~ s/\s+//g;
+    $name     =~ s/\s+//g;
+    $lane     =~ s/\s+//g;
+    $index    =~ s/\s+//g;
+    $flowcell =~ s/\s+//g;
+
     if ($samples{$name}) {
         die "There are multiple $name in $ss sheet";
     }