From 1dfac52fad1c44c861e40ccdeffd7aa07860b0e2 Mon Sep 17 00:00:00 2001
From: rdemko2332 <rdemko2332@gmail.com>
Date: Wed, 9 Sep 2026 15:22:27 -0400
Subject: [PATCH 1/3] Add shared, opt-in cluster nextflow config via
 includeConfig

New WorkflowStep.pm helper getSharedClusterNextflowConfigIncludeBlock(): reads
$clusterServer.sharedNextflowConfig from stepsShared.prop (via getSharedConfigRelaxed,
so an unset value is a silent no-op) and, if set, returns an includeConfig line pulling
in that cluster-provided config file. Lets a cluster-wide nextflow process{} setting
(e.g. beforeScript = 'module load apptainer/1.4.1 && unset LD_LIBRARY_PATH') be rolled
out via a one-line stepsShared.prop change instead of hand-editing every
Make*NextflowConfig.pm generator -- 37 of them exist, and this session's ortho work
already needed the same beforeScript line added to 7 by hand.

Mirrors the existing getNextflowLsfScratchEnvBlock() pattern in the same file (same
shared-helper shape, already called identically from 28 of the 37 generators).

Also fixed getNextflowLsfScratchEnvBlock() while here: NXF_SCRATCH = '$LSF_TMPDIR' had
no default, crashing under nextflow's own set -u if LSF doesn't export LSF_TMPDIR --
the same bug independently found and hand-fixed in 7 ortho-specific generators on
another branch this session. Centralizing the fix here covers all 28 current callers.
---
 Main/lib/perl/WorkflowSteps/WorkflowStep.pm | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/Main/lib/perl/WorkflowSteps/WorkflowStep.pm b/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
index 998887ce1b..6ab10a99bb 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";
 }
 
 

From da29ef678ba8dbeded4105b472c50a84555b730e Mon Sep 17 00:00:00 2001
From: rdemko2332 <rdemko2332@gmail.com>
Date: Wed, 9 Sep 2026 15:27:56 -0400
Subject: [PATCH 2/3] Wire the shared cluster nextflow config include into
 every config generator

Every Make*NextflowConfig.pm step class (38 total) now computes
$sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock() and
interpolates it at the very top of its generated nextflow config, before params {}.
When $clusterServer.sharedNextflowConfig isn't set in stepsShared.prop this renders as
an empty string -- verified byte-identical output to before this change for that
(default, current) case. When it is set, an includeConfig '<path>' line appears at the
top, pulling in whatever cluster-wide process{} settings that shared file declares.

Mechanical, per-file changes only: add the one declaration line (anchored next to each
file's existing $lsfEnv/$lsfScratch computation, or near the top of run() for the 5
files with neither), and prepend $sharedClusterConfig to whatever the file already
prints (either interpolated into a heredoc string, or concatenated onto a $configString
variable) -- every file's own existing style preserved as-is, nothing else changed.

The 5 ortho-specific generators here still hand-roll their own $lsfScratch (predates the
shared getNextflowLsfScratchEnvBlock() helper 28 of the others already use) -- left
untouched, out of scope for this change.
---
 Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm   | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeArbaNextflowConfig.pm        | 3 ++-
 .../WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm     | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm   | 3 ++-
 .../perl/WorkflowSteps/MakeBlastSimilarityNextflowConfig.pm  | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm        | 3 ++-
 .../perl/WorkflowSteps/MakeBowtieMappingNextflowConfig.pm    | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeBulkRnaSeqNextflowConfig.pm  | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeBuscoNextflowConfig.pm       | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeChipSeqNextflowConfig.pm     | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeDnaSeqLoadNextflowConfig.pm  | 3 ++-
 .../MakeDnaSeqMergeExperimentsNextflowConfig.pm              | 4 +++-
 Main/lib/perl/WorkflowSteps/MakeDnaSeqNextflowConfig.pm      | 3 ++-
 .../MakeDnaSeqSingleExperimentNextflowConfig.pm              | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeDustNextflowConfig.pm        | 3 ++-
 .../perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm   | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm  | 3 ++-
 .../MakeGenomicArrayExperimentNextflowConfig.pm              | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeIprscan5NextflowConfig.pm    | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeLoadCNVNextflowConfig.pm     | 5 +++--
 .../perl/WorkflowSteps/MakeLongReadRnaSeqNextflowConfig.pm   | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeMassSpecNextflowConfig.pm    | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeNgsSamplesNextflowConfig.pm  | 3 ++-
 .../WorkflowSteps/MakeOriginsOfReplicationNextflowConfig.pm  | 3 ++-
 .../perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm  | 3 ++-
 .../MakeOrthoFinderPeripheralEntryNextflowConfig.pm          | 3 ++-
 .../MakeOrthoFinderPostProcessingEntryNextflowConfig.pm      | 3 ++-
 .../MakeOrthoFinderPostResidualEntryNextflowConfig.pm        | 3 ++-
 .../MakeOrthoFinderResidualEntryNextflowConfig.pm            | 3 ++-
 .../WorkflowSteps/MakeProteinAttributesNextflowConfig.pm     | 3 ++-
 Main/lib/perl/WorkflowSteps/MakePsiPredNextflowConfig.pm     | 3 ++-
 .../lib/perl/WorkflowSteps/MakeRepeatMaskerNextflowConfig.pm | 3 ++-
 .../perl/WorkflowSteps/MakeRnaSeqAnalysisNextflowConfig.pm   | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeSegNextflowConfig.pm         | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeSignalPNextflowConfig.pm     | 3 ++-
 .../MakeSplicedLeaderAndPolyASitesNextflowConfig.pm          | 3 ++-
 .../WorkflowSteps/MakeStudyAssayResultsNextflowConfig.pm     | 3 ++-
 Main/lib/perl/WorkflowSteps/MakeTmhmmNextflowConfig.pm       | 3 ++-
 38 files changed, 78 insertions(+), 39 deletions(-)

diff --git a/Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm
index 62e0798340..c4bcaaf44a 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 96ae7f6574..8d581a1764 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 708c514b1d..e6ef3cc5af 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 72bb881532..fc69e1b7cc 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 146951f896..a6fda4b9bd 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 5eb18bb34d..80880b10b8 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 019fb29d82..d5ed0d1f7d 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 82d9172dee..3cf90aeb0d 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 1818fe9cd1..1db868bfab 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 cad7e2c449..4a82290fee 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 33b1569eb9..02d8d2db35 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 96826797f3..4078f5962e 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 67a8d301c6..546fafe539 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 77d500edbc..45c7f91cbf 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 bed70acdb9..20080dc8bf 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 25e62038f4..85009ac9af 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 70b7cc7dec..ffe64f4aa9 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 f51dc51b3e..ae8126b756 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 26ea98f04c..369d1ca2e5 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 27a40f55f5..e835a134be 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 1b5fe3bcf2..d90169733e 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 de70b5b198..1d901307d4 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 57dae80bb8..036c74f6ee 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 c136215632..6ac48b8bdc 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 5e2ee0680f..94022e40ae 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 f1dfda6769..9297b7652f 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 de0dd87491..9a1052e695 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 86b43545ed..0349af1779 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 0a88f349c0..e944b38dbe 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 cb06d8b4c6..d5cb1bdfcf 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 867ef563fe..e53219e6dc 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 f1ed5da6c9..7e2629f577 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 462684452a..8445662d85 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 a63c2889b6..4352825982 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 bde902ca0f..36ebdff9eb 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 153b3e73e1..4d5d42ce3e 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 fb9d9550a7..c47c54365f 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 e6e83f5ecc..33f7212628 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);
   }
 }

From d1c70181c6e98d4fb2cbfddbefc368e351728e6c Mon Sep 17 00:00:00 2001
From: rdemko2332 <rdemko2332@gmail.com>
Date: Thu, 10 Sep 2026 12:50:53 -0400
Subject: [PATCH 3/3] Shared nextflow config lives on the workflow server,
 symlinked into analysisDir

Reworks getSharedClusterNextflowConfigIncludeBlock() (added earlier this branch): the
shared config file now lives on the workflow server (yew), read from a flat
'sharedNextflowConfig' key in stepsShared.prop, not a $clusterServer-scoped cluster path.
Decouples the file's location from which cluster runs the work.

Mechanism: the helper symlinks the yew-side file into the run's analysisDir as
sharedNextflow.config, then returns an includeConfig line pointing at that file's
cluster-side path (translated via relativePathToNextflowClusterPath, same as every other
path these generators emit). CopyNextflowWorkingDirToCluster later tars analysisDir to
the cluster with 'tar cfh' -- the -h dereferences the symlink into real content there, so
the includeConfig target exists on the cluster.

Signature gains ($analysisDir, $workingDirRelativePath) -- the caller's own locals, needed
to place the symlink and translate the path. A caller that can't supply them (the 33
non-ortho generators, still calling zero-arg from the earlier sweep) gets a silent no-op,
same as when the key is unset. Wired for real only in the 5 ortho generators for now;
extending to other workflows is a separate change.

Errors early with a clear message if sharedNextflowConfig points at a nonexistent file,
rather than failing later in an opaque tar error.
---
 .../MakeOrthoFinderCoreNextflowConfig.pm      |  2 +-
 ...rthoFinderPeripheralEntryNextflowConfig.pm |  2 +-
 ...FinderPostProcessingEntryNextflowConfig.pm |  2 +-
 ...hoFinderPostResidualEntryNextflowConfig.pm |  2 +-
 ...eOrthoFinderResidualEntryNextflowConfig.pm |  2 +-
 Main/lib/perl/WorkflowSteps/WorkflowStep.pm   | 39 +++++++++++++------
 6 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm
index 94022e40ae..c96c689fab 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderCoreNextflowConfig.pm
@@ -31,7 +31,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
-  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock($analysisDir, $workingDirRelativePath);
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm
index 9297b7652f..7d4ac60b10 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPeripheralEntryNextflowConfig.pm
@@ -37,7 +37,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
-  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock($analysisDir, $workingDirRelativePath);
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm
index 9a1052e695..1d471fd396 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostProcessingEntryNextflowConfig.pm
@@ -42,7 +42,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
-  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock($analysisDir, $workingDirRelativePath);
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm
index 0349af1779..e336e613f2 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderPostResidualEntryNextflowConfig.pm
@@ -33,7 +33,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
-  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock($analysisDir, $workingDirRelativePath);
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
diff --git a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm
index e944b38dbe..0ec308d872 100644
--- a/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm
+++ b/Main/lib/perl/WorkflowSteps/MakeOrthoFinderResidualEntryNextflowConfig.pm
@@ -23,7 +23,7 @@ sub run {
 
   my $executor = $self->getClusterExecutor();
   my $lsfScratch = ($executor eq 'lsf') ? "\n  NXF_SCRATCH = '\$LSF_TMPDIR'" : '';
-  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
+  my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock($analysisDir, $workingDirRelativePath);
   my $queue = $self->getClusterQueue();
 
   if ($undo) {
diff --git a/Main/lib/perl/WorkflowSteps/WorkflowStep.pm b/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
index 6ab10a99bb..84b0e69fbc 100644
--- a/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
+++ b/Main/lib/perl/WorkflowSteps/WorkflowStep.pm
@@ -353,19 +353,36 @@ sub getNextflowLsfScratchEnvBlock {
   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
+# Opt-in include of a shared 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.
+# every Make*NextflowConfig.pm generator by hand).
+#
+# The file lives on the workflow server (yew), not the cluster, so which cluster actually
+# runs the processing can change without moving it. It is symlinked into the run's
+# analysisDir here; CopyNextflowWorkingDirToCluster later carries analysisDir to the
+# cluster with 'tar cfh', whose -h dereferences the symlink into real content there. The
+# returned line then points includeConfig at that file's cluster-side path, translated the
+# same way every other path these generators emit is.
+#
+# Reads the flat 'sharedNextflowConfig' key from stepsShared.prop (via getSharedConfigRelaxed,
+# so unset is a silent no-op -- existing builds are unaffected). $analysisDir and
+# $workingDirRelativePath are the calling generator's own locals; a caller that doesn't
+# have them (i.e. can't place the symlink) also gets a silent no-op.
 sub getSharedClusterNextflowConfigIncludeBlock {
-  my ($self) = @_;
-  my $clusterServer = $self->getSharedConfig('clusterServer');
-  my $path = $self->getSharedConfigRelaxed("$clusterServer.sharedNextflowConfig");
-  return '' unless $path;
-  return "includeConfig '$path'\n";
+  my ($self, $analysisDir, $workingDirRelativePath) = @_;
+
+  my $sharedPath = $self->getSharedConfigRelaxed('sharedNextflowConfig');
+  return '' unless $sharedPath;
+  return '' unless $analysisDir && $workingDirRelativePath;
+
+  $self->error("sharedNextflowConfig '$sharedPath' does not exist on the workflow server")
+    unless -e $sharedPath;
+
+  my $localLink = join("/", $self->getWorkflowDataDir(), $analysisDir, "sharedNextflow.config");
+  $self->runCmd(0, "ln -sfn $sharedPath $localLink");
+
+  my $clusterPath = $self->relativePathToNextflowClusterPath($workingDirRelativePath, "$analysisDir/sharedNextflow.config");
+  return "includeConfig '$clusterPath'\n";
 }