diff --git a/Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm
index 62e079834..c4bcaaf44 100644
--- a/Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm
@@ -28,6 +28,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
 
     if ($undo) {
@@ -36,7 +37,7 @@ sub run {
 	open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   fasta = \"$digestedFasta\"
   gff = \"$digestedGff\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeArbaNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeArbaNextflowConfig.pm
index 96ae7f657..8d581a176 100644
--- a/Main/lib/perl/WorkflowSteps/MakeArbaNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeArbaNextflowConfig.pm
@@ -26,6 +26,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
 
     if ($undo) {
@@ -34,7 +35,7 @@ sub run {
 	open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   interproResults = \"$digestedInterproResults\"
   outputDir = \"$digestedOutputDir\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm
index 708c514b1..e6ef3cc5a 100644
--- a/Main/lib/perl/WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm
@@ -71,6 +71,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -121,7 +122,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm
index 72bb88153..fc69e1b7c 100644
--- a/Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm
@@ -31,6 +31,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -70,7 +71,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeBlastSimilarityNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeBlastSimilarityNextflowConfig.pm
index 146951f89..a6fda4b9b 100644
--- a/Main/lib/perl/WorkflowSteps/MakeBlastSimilarityNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeBlastSimilarityNextflowConfig.pm
@@ -38,6 +38,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
  
     if ($undo) {
@@ -46,7 +47,7 @@ sub run {
 	open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   blastProgram = \"$blastProgram\"
   seqFile = \"$seqFile\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm
index 5eb18bb34..80880b10b 100644
--- a/Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm
@@ -31,6 +31,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
 
     my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -67,7 +68,7 @@ process {
 includeConfig "$clusterConfigFile"
 NEXTFLOW
 
-    print F $configString . $lsfEnv;
+    print F $sharedClusterConfig . $configString . $lsfEnv;
     close(F);
     }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeBowtieMappingNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeBowtieMappingNextflowConfig.pm
index 019fb29d8..d5ed0d1f7 100644
--- a/Main/lib/perl/WorkflowSteps/MakeBowtieMappingNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeBowtieMappingNextflowConfig.pm
@@ -32,6 +32,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
@@ -40,7 +41,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   preconfiguredDatabase = $preconfiguredDatabase
   writeBedFile = $writeBedFile
diff --git a/Main/lib/perl/WorkflowSteps/MakeBulkRnaSeqNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeBulkRnaSeqNextflowConfig.pm
index 82d9172de..3cf90aeb0 100644
--- a/Main/lib/perl/WorkflowSteps/MakeBulkRnaSeqNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeBulkRnaSeqNextflowConfig.pm
@@ -36,6 +36,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -101,7 +102,7 @@ def check_max(obj, type) {
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeBuscoNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeBuscoNextflowConfig.pm
index 1818fe9cd..1db868bfa 100644
--- a/Main/lib/perl/WorkflowSteps/MakeBuscoNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeBuscoNextflowConfig.pm
@@ -30,6 +30,7 @@ sub run {
     
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
     my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -67,7 +68,7 @@ process {
 includeConfig "$clusterConfigFile"
 
 NEXTFLOW
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
     }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeChipSeqNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeChipSeqNextflowConfig.pm
index cad7e2c44..4a82290fe 100644
--- a/Main/lib/perl/WorkflowSteps/MakeChipSeqNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeChipSeqNextflowConfig.pm
@@ -40,6 +40,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -83,7 +84,7 @@ process {
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeDnaSeqLoadNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeDnaSeqLoadNextflowConfig.pm
index 33b1569eb..02d8d2db3 100644
--- a/Main/lib/perl/WorkflowSteps/MakeDnaSeqLoadNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeDnaSeqLoadNextflowConfig.pm
@@ -14,13 +14,14 @@ sub run {
     my $genomeExtDbRlsSpec = $self->getParamValue("genomeExtDbRlsSpec");
 
     my $configPath = $self->getWorkflowDataDir() . "/" . $self->getParamValue("nextflowConfigFile");
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
     if ($undo) {
         $self->runCmd(0, "rm -rf $configPath");
     } else {
         open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
         print F
-"
+"$sharedClusterConfig
 params {
   indelDir          = \"$indelDir\"
   extDbRlsSpec      = '\"$extDbRlsSpec\"'
diff --git a/Main/lib/perl/WorkflowSteps/MakeDnaSeqMergeExperimentsNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeDnaSeqMergeExperimentsNextflowConfig.pm
index 96826797f..4078f5962 100644
--- a/Main/lib/perl/WorkflowSteps/MakeDnaSeqMergeExperimentsNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeDnaSeqMergeExperimentsNextflowConfig.pm
@@ -63,9 +63,11 @@ sub run {
   my @experimentConfigs = glob($experimentConfigGlob);
   my $ploidy = parsePloidyFromConfigs(@experimentConfigs);
 
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
+
   open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
   print F
-"
+"$sharedClusterConfig
 params {
 
   outputDir       = \"$outputDir\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeDnaSeqNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeDnaSeqNextflowConfig.pm
index 67a8d301c..546fafe53 100644
--- a/Main/lib/perl/WorkflowSteps/MakeDnaSeqNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeDnaSeqNextflowConfig.pm
@@ -39,6 +39,7 @@ sub run {
     my $executor        = $self->getClusterExecutor();
     my $queue           = $self->getClusterQueue();
     my $lsfEnv          = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
     my $genomeFastaFile = $self->getWorkflowDataDir() . "/" . $self->getParamValue("genomeFastaFile");
 
@@ -59,7 +60,7 @@ sub run {
         $self->runCmd(0, "rm -rf $nextflowConfigFile");
     } else {
         open(F, ">", $nextflowConfigFile) or die "$! :Can't open config file '$nextflowConfigFile' for writing";
-        print F "
+        print F "$sharedClusterConfig
 params {
   samplesheet              = \"$digestedSampleSheet\"
   bwaThreads               = $bwaThreads
diff --git a/Main/lib/perl/WorkflowSteps/MakeDnaSeqSingleExperimentNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeDnaSeqSingleExperimentNextflowConfig.pm
index 77d500edb..45c7f91cb 100644
--- a/Main/lib/perl/WorkflowSteps/MakeDnaSeqSingleExperimentNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeDnaSeqSingleExperimentNextflowConfig.pm
@@ -42,6 +42,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $gusConfigFile = $ENV{GUS_HOME}."/config/gus.config";
@@ -75,7 +76,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   input = \"$input\"
   fromBAM = $fromBAM
diff --git a/Main/lib/perl/WorkflowSteps/MakeDustNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeDustNextflowConfig.pm
index bed70acdb..20080dc8b 100644
--- a/Main/lib/perl/WorkflowSteps/MakeDustNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeDustNextflowConfig.pm
@@ -26,6 +26,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -53,7 +54,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm
index 25e62038f..85009ac9a 100644
--- a/Main/lib/perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm
@@ -36,6 +36,7 @@ sub run {
     my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
     my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -92,7 +93,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-        print F $configString . $lsfEnv;
+        print F $sharedClusterConfig . $configString . $lsfEnv;
         close(F);
     }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm
index 70b7cc7de..ffe64f4aa 100644
--- a/Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm
@@ -21,6 +21,7 @@ sub run {
     my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -51,7 +52,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeGenomicArrayExperimentNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeGenomicArrayExperimentNextflowConfig.pm
index f51dc51b3..ae8126b75 100644
--- a/Main/lib/perl/WorkflowSteps/MakeGenomicArrayExperimentNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeGenomicArrayExperimentNextflowConfig.pm
@@ -47,6 +47,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -78,7 +79,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeIprscan5NextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeIprscan5NextflowConfig.pm
index 26ea98f04..369d1ca2e 100644
--- a/Main/lib/perl/WorkflowSteps/MakeIprscan5NextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeIprscan5NextflowConfig.pm
@@ -25,6 +25,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
 
     if ($undo) {
@@ -33,7 +34,7 @@ sub run {
 	open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   input = \"$digestedInput\"
   outputDir = \"$digestedOutputDir\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeLoadCNVNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeLoadCNVNextflowConfig.pm
index 27a40f55f..e835a134b 100644
--- a/Main/lib/perl/WorkflowSteps/MakeLoadCNVNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeLoadCNVNextflowConfig.pm
@@ -16,7 +16,8 @@ sub run {
   my $footprintFile = join("/", $workflowDataDir, $self->getParamValue("footprintFile"));
   my $ploidy = $self->getParamValue("ploidy");
   my $taxonId = $self->getParamValue("taxonId");
-  my $outputDir = join("/", $workflowDataDir, $self->getParamValue("clusterResultDir"));   
+  my $outputDir = join("/", $workflowDataDir, $self->getParamValue("clusterResultDir"));
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
   if ($undo) {
     $self->runCmd(0,"rm -rf $configPath");
@@ -24,7 +25,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   input = \"$input\"
   outputDir = \"$outputDir\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeLongReadRnaSeqNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeLongReadRnaSeqNextflowConfig.pm
index 1b5fe3bcf..d90169733 100644
--- a/Main/lib/perl/WorkflowSteps/MakeLongReadRnaSeqNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeLongReadRnaSeqNextflowConfig.pm
@@ -42,6 +42,7 @@ sub run {
     my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
 
     my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -52,7 +53,7 @@ sub run {
     } else {
         open(F, ">", $nextflowConfigFile) or die "$! :Can't open config file '$nextflowConfigFile' for writing";
         print F
-            "
+            "$sharedClusterConfig
 params {
     input = \"$digestedInputDirPath\"
     samplesheetFileName = \"$sampleSheet\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeMassSpecNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeMassSpecNextflowConfig.pm
index de70b5b19..1d901307d 100644
--- a/Main/lib/perl/WorkflowSteps/MakeMassSpecNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeMassSpecNextflowConfig.pm
@@ -34,6 +34,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -64,7 +65,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeNgsSamplesNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeNgsSamplesNextflowConfig.pm
index 57dae80bb..036c74f6e 100644
--- a/Main/lib/perl/WorkflowSteps/MakeNgsSamplesNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeNgsSamplesNextflowConfig.pm
@@ -39,6 +39,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -100,7 +101,7 @@ workDir = "$digestedAnalysisDirPath/ngs-samples-work"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeOriginsOfReplicationNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOriginsOfReplicationNextflowConfig.pm
index c13621563..6ac48b8bd 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOriginsOfReplicationNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOriginsOfReplicationNextflowConfig.pm
@@ -38,6 +38,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -82,7 +83,7 @@ process {
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm
index 5e2ee0680..94022e40a 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm
@@ -31,6 +31,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
@@ -39,7 +40,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
   proteomes = \"$proteomesInNextflowWorkingDirOnCluster\"
   outputDir = \"$resultsDirectoryInNextflowWorkingDirOnCluster\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm
index f1dfda676..9297b7652 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm
@@ -37,6 +37,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
@@ -45,7 +46,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
     outputDir = \"$resultsDirectoryInNextflowWorkingDirOnCluster\"
     coreProteomes = \"$coreProteomesInNextflowWorkingDirOnCluster\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm
index de0dd8749..9a1052e69 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm
@@ -42,6 +42,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
@@ -50,7 +51,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
     outputDir = \"$resultsDirectoryInNextflowWorkingDirOnCluster\"
     residualFasta  = \"$residualFastaInNextflowWorkingDirOnCluster\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm
index 86b43545e..0349af177 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm
@@ -33,6 +33,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
@@ -41,7 +42,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
     outputDir = \"$resultsDirectoryInNextflowWorkingDirOnCluster\"
     residualFasta = \"$residualFastaInNextflowWorkingDirOnCluster\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm
index 0a88f349c..e944b38db 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm
@@ -23,6 +23,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
@@ -31,7 +32,7 @@ sub run {
     open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";
 
     print F
-"
+"$sharedClusterConfig
 params {
     outputDir = \"$resultsDirectoryInNextflowWorkingDirOnCluster\"
     residualFastaDir = \"$residualFastaDirInNextflowWorkingDirOnCluster\"
diff --git a/Main/lib/perl/WorkflowSteps/MakeProteinAttributesNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeProteinAttributesNextflowConfig.pm
index cb06d8b4c..d5cb1bdfc 100644
--- a/Main/lib/perl/WorkflowSteps/MakeProteinAttributesNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeProteinAttributesNextflowConfig.pm
@@ -23,6 +23,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -53,7 +54,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakePsiPredNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakePsiPredNextflowConfig.pm
index 867ef563f..e53219e6d 100644
--- a/Main/lib/perl/WorkflowSteps/MakePsiPredNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakePsiPredNextflowConfig.pm
@@ -23,6 +23,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
     my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -56,7 +57,7 @@ process {
 includeConfig "$clusterConfigFile"
 
 NEXTFLOW
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
 	close(F);
     }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeRepeatMaskerNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeRepeatMaskerNextflowConfig.pm
index f1ed5da6c..7e2629f57 100644
--- a/Main/lib/perl/WorkflowSteps/MakeRepeatMaskerNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeRepeatMaskerNextflowConfig.pm
@@ -39,6 +39,7 @@ sub run {
 
     my $executor = $self->getClusterExecutor();
     my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+    my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
     my $queue = $self->getClusterQueue();
     my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -87,7 +88,7 @@ singularity {
 
 
 NEXTFLOW
-    print F $configString . $lsfEnv;
+    print F $sharedClusterConfig . $configString . $lsfEnv;
     close(F);
 
     }
diff --git a/Main/lib/perl/WorkflowSteps/MakeRnaSeqAnalysisNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeRnaSeqAnalysisNextflowConfig.pm
index 462684452..8445662d8 100644
--- a/Main/lib/perl/WorkflowSteps/MakeRnaSeqAnalysisNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeRnaSeqAnalysisNextflowConfig.pm
@@ -25,6 +25,7 @@ sub run {
   my $workflowDataDir = $self->getWorkflowDataDir();
 
   my $baseConfigFile = "\$baseDir/conf/singularity.config";
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
   if ($undo) {
       $self->runCmd(0, "rm $workflowDataDir/$nextflowConfigFile");
@@ -48,7 +49,7 @@ includeConfig "$baseConfigFile"
 
 NEXTFLOW
 
-      print F $configString;
+      print F $sharedClusterConfig . $configString;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeSegNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeSegNextflowConfig.pm
index a63c2889b..435282598 100644
--- a/Main/lib/perl/WorkflowSteps/MakeSegNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeSegNextflowConfig.pm
@@ -22,6 +22,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -52,7 +53,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeSignalPNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeSignalPNextflowConfig.pm
index bde902ca0..36ebdff9e 100644
--- a/Main/lib/perl/WorkflowSteps/MakeSignalPNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeSignalPNextflowConfig.pm
@@ -36,6 +36,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -79,7 +80,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeSplicedLeaderAndPolyASitesNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeSplicedLeaderAndPolyASitesNextflowConfig.pm
index 153b3e73e..4d5d42ce3 100644
--- a/Main/lib/perl/WorkflowSteps/MakeSplicedLeaderAndPolyASitesNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeSplicedLeaderAndPolyASitesNextflowConfig.pm
@@ -37,6 +37,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
 
@@ -77,7 +78,7 @@ process {
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeStudyAssayResultsNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeStudyAssayResultsNextflowConfig.pm
index fb9d9550a..c47c54365 100644
--- a/Main/lib/perl/WorkflowSteps/MakeStudyAssayResultsNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeStudyAssayResultsNextflowConfig.pm
@@ -24,6 +24,7 @@ sub run {
   my $workflowDataDir = $self->getWorkflowDataDir();
 
   my $baseConfigFile = "\$baseDir/conf/singularity.config";
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
 
   # Determine the input file based on platform mapping (logic from DoStudyAssayResults)
   my $inputFile;
@@ -74,7 +75,7 @@ $configString .= <<NEXTFLOW;
 includeConfig "$baseConfigFile"
 NEXTFLOW
 
-      print F $configString;
+      print F $sharedClusterConfig . $configString;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/MakeTmhmmNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeTmhmmNextflowConfig.pm
index e6e83f5ec..33f721262 100644
--- a/Main/lib/perl/WorkflowSteps/MakeTmhmmNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeTmhmmNextflowConfig.pm
@@ -29,6 +29,7 @@ sub run {
   my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
   my $executor = $self->getClusterExecutor();
   my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
   my $queue = $self->getClusterQueue();
 
   my $clusterConfigFile = "\$baseDir/conf/${executor}.config";
@@ -64,7 +65,7 @@ includeConfig "$clusterConfigFile"
 
 NEXTFLOW
 
-      print F $configString . $lsfEnv;
+      print F $sharedClusterConfig . $configString . $lsfEnv;
       close(F);
   }
 }
diff --git a/Main/lib/perl/WorkflowSteps/WorkflowStep.pm b/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
index 998887ce1..6ab10a99b 100644
--- a/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
+++ b/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
@@ -348,7 +348,24 @@ sub getClusterExecutor {
 sub getNextflowLsfScratchEnvBlock {
   my ($self) = @_;
   return '' unless $self->getClusterExecutor() eq 'lsf';
-  return "\nenv {\n  NXF_SCRATCH = '\$LSF_TMPDIR'\n}\n";
+  # LSF_TMPDIR isn't guaranteed to be exported by every LSF cluster/job; without the
+  # ':-' default this crashes under nextflow's own 'set -u' if it's ever unset.
+  return "\nenv {\n  NXF_SCRATCH = '\${LSF_TMPDIR:-}'\n}\n";
+}
+
+# Opt-in include of a shared, cluster-provided nextflow config file (e.g. one that sets
+# process { beforeScript = '...' } for module loads that shouldn't have to be repeated in
+# every Make*NextflowConfig.pm generator by hand). Reads $clusterServer.sharedNextflowConfig
+# from stepsShared.prop; if it isn't set, this is a silent no-op -- existing builds that
+# don't configure it are unaffected. If it is set, the returned line pulls that config in
+# via nextflow's own includeConfig directive, so a single shared file can add or change a
+# cluster-wide setting without touching every step class that generates a nextflow config.
+sub getSharedClusterNextflowConfigIncludeBlock {
+  my ($self) = @_;
+  my $clusterServer = $self->getSharedConfig('clusterServer');
+  my $path = $self->getSharedConfigRelaxed("$clusterServer.sharedNextflowConfig");
+  return '' unless $path;
+  return "includeConfig '$path'\n";
 }