Put the --import-file back

Skyline needs the path to locate the LC-MS files not in the work dir. Removed by e960094
Nesvilab · Oct 11, 2024 · efd169d · efd169d
1 parent 2a09902
commit efd169d
Showing 1 changed file with 2 additions and 5 deletions.
diff --git a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java b/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java
@@ -255,11 +255,8 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
         writer.write("--full-scan-isolation-scheme=\"Results only\" ");
       }
 
-      if (dataType.contentEquals("DIA") && overridePeakBounds) {
-        // lc-ms file import is automatic when reading peptide list, but needs the DIA files imported separated for DIA SSL
-        for (String s : lcmsFiles) {
-          writer.write("--import-file=" + s + " ");
-        }
+      for (String s : lcmsFiles) {
+        writer.write("--import-file=" + s + " ");
       }
 
       // todo: waiting for a fix (or clarification) from Brendan. Skyline does not allow this unless fasta has been imported