Save manifest and workflow files before running anything.

Some tools might need those files.

Author: fcyu

MSFragger-GUI/src/com/dmtavt/fragpipe/FragpipeRun.java

@@ -331,6 +331,12 @@ public static int run(MessageRun m) {
       toConsole("LCMS files:\n" + createLcmsFilesString(lcmsFileGroups), tabRun.console);
       toConsole("", tabRun.console);
 
+      // save manifest file in both GUI and headless mode
+      Path pp = wd.resolve("fragpipe-files" + manifestExt);
+      Bus.post(new MessageManifestSave(pp, true));
+
+      saveRuntimeConfig(wd);
+
       // Converting process builders descriptors to process builder infos
       final List<ProcessBuilderInfo> pbis = pbDescsBuilderDescs.stream()
           .flatMap(pbd -> pbd.pbis.stream().map(pbi ->
@@ -507,11 +513,6 @@ public static int run(MessageRun m) {
         String totalTime = String.format("%.1f", (System.nanoTime() - startTime) * 1e-9 / 60);
         toConsole(Fragpipe.COLOR_RED_DARKEST, "\n=============================================================ALL JOBS DONE IN " + totalTime + " MINUTES=============================================================", true, tabRun.console);
         Bus.post(MessageSaveLog.saveInDir(wd));
-        saveRuntimeConfig(wd);
-
-        // save manifest file in both GUI and headless mode
-        Path path = wd.resolve("fragpipe-files" + manifestExt);
-        Bus.post(new MessageManifestSave(path, true));
 
         if (tabRun.isWriteSubMzml()) { // write sub workflow and manifest files for the second-pass
           try {

MSFragger-GUI/src/com/dmtavt/fragpipe/cmd/ProcessBuilderInfo.java

@@ -18,14 +18,11 @@
 package com.dmtavt.fragpipe.cmd;
 
 import static com.dmtavt.fragpipe.messages.MessagePrintToConsole.toConsole;
-import static com.dmtavt.fragpipe.tabs.TabWorkflow.manifestExt;
 
 import com.dmtavt.fragpipe.Fragpipe;
-import com.dmtavt.fragpipe.FragpipeRun;
 import com.dmtavt.fragpipe.api.Bus;
 import com.dmtavt.fragpipe.messages.MessageKillAll;
 import com.dmtavt.fragpipe.messages.MessageKillAll.REASON;
-import com.dmtavt.fragpipe.messages.MessageManifestSave;
 import com.dmtavt.fragpipe.messages.MessageSaveLog;
 import com.dmtavt.fragpipe.process.ProcessResult;
 import com.github.chhh.utils.swing.TextConsole;
@@ -135,14 +132,6 @@ public static Runnable toRunnable(final ProcessBuilderInfo pbi, final Path wdPat
               toConsole(Fragpipe.COLOR_RED, "Process returned non-zero exit code, stopping", true, console);
               Bus.post(new MessageKillAll(REASON.NON_ZERO_RETURN_FROM_PROCESS, console));
               Bus.post(MessageSaveLog.saveInDir(wdPath));
-              FragpipeRun.saveRuntimeConfig(wdPath);
-
-              if (!isDownstream) {
-                // save manifest file in both GUI and headless mode
-                Path path = wdPath.resolve("fragpipe-files" + manifestExt);
-                Bus.post(new MessageManifestSave(path, true));
-              }
-
               break;
             }
           } catch (IllegalThreadStateException ex) {