data/download_tools_longread.sh: added StraglrOn

src/NGS/runqc_parser_ont.php: allow manual exclusion of analysis folders
imgag · Sep 9, 2024 · d735ef8 · d735ef8
1 parent 6768396
commit d735ef8
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/data/download_tools_longread.sh b/data/download_tools_longread.sh
@@ -85,7 +85,12 @@ tar xzf straglr-1.5.1.tar.gz
 mv straglr straglr-1.5.1
 rm straglr-1.5.1.tar.gz
 
-#TODO: StraglrOn
+#download StraglrOn
+cd $folder
+git clone https://github.com/imgag/StraglrOn.git StraglrOn_v0.2.2
+cd StraglrOn_v0.2.2
+git checkout "v0.2.2"
+cd ..
 
 #download Tandem Repeats Finder
 cd $folder

diff --git a/src/NGS/runqc_parser_ont.php b/src/NGS/runqc_parser_ont.php
@@ -29,7 +29,7 @@
 if (!ends_with($run_dir, substr($name, 1))) trigger_error("Run folder name ('".basename2($run_dir)."') doesn't match run name ({$name}!", E_USER_ERROR);
 
 // check fcid and raw data folder
-$fc_dir = glob("{$run_dir}/*_{$flowcell_id}_*");
+$fc_dir = glob("{$run_dir}/2*_{$flowcell_id}_*");
 if (count($fc_dir) == 0) trigger_error("Run raw data folder missing or wrong FlowCell ID in NGSD!", E_USER_ERROR);
 if (count($fc_dir) > 1) trigger_error("Multiple raw data found!\n".implode(", ", $fc_dir), E_USER_ERROR);
 $fc_dir = $fc_dir[0];