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Shared cluster nextflow config #102

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1dfac52
Add shared, opt-in cluster nextflow config via includeConfig
rdemko2332 Sep 9, 2026
da29ef6
Wire the shared cluster nextflow config include into every config gen…
rdemko2332 Sep 9, 2026
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3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeAntismashNextflowConfig.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ sub run {

my $executor = $self->getClusterExecutor();
my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
my $queue = $self->getClusterQueue();

if ($undo) {
Expand All @@ -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\"
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeArbaNextflowConfig.pm
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Expand Up @@ -26,6 +26,7 @@ sub run {

my $executor = $self->getClusterExecutor();
my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
my $queue = $self->getClusterQueue();

if ($undo) {
Expand All @@ -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\"
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -121,7 +122,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeBlastPPdbNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -70,7 +71,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeBlastSimilarityNextflowConfig.pm
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Expand Up @@ -38,6 +38,7 @@ sub run {

my $executor = $self->getClusterExecutor();
my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
my $queue = $self->getClusterQueue();

if ($undo) {
Expand All @@ -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\"
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeBlatNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -67,7 +68,7 @@ process {
includeConfig "$clusterConfigFile"
NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeBowtieMappingNextflowConfig.pm
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Expand Up @@ -32,6 +32,7 @@ sub run {

my $executor = $self->getClusterExecutor();
my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
my $queue = $self->getClusterQueue();

if ($undo) {
Expand All @@ -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
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeBulkRnaSeqNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -101,7 +102,7 @@ def check_max(obj, type) {

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeBuscoNextflowConfig.pm
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Expand Up @@ -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";

Expand Down Expand Up @@ -67,7 +68,7 @@ process {
includeConfig "$clusterConfigFile"

NEXTFLOW
print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeChipSeqNextflowConfig.pm
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Expand Up @@ -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";

Expand Down Expand Up @@ -83,7 +84,7 @@ process {

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeDnaSeqLoadNextflowConfig.pm
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Expand Up @@ -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\"'
Expand Down
4 changes: 3 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeDnaSeqMergeExperimentsNextflowConfig.pm
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Expand Up @@ -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\"
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeDnaSeqNextflowConfig.pm
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Expand Up @@ -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");

Expand All @@ -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
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeDnaSeqSingleExperimentNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeDustNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -53,7 +54,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeEpitopeMappingNextflowConfig.pm
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Expand Up @@ -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";

Expand Down Expand Up @@ -92,7 +93,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeExportpredNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -51,7 +52,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeGenomicArrayExperimentNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -78,7 +79,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeIprscan5NextflowConfig.pm
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Expand Up @@ -25,6 +25,7 @@ sub run {

my $executor = $self->getClusterExecutor();
my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();
my $sharedClusterConfig = $self->getSharedClusterNextflowConfigIncludeBlock();
my $queue = $self->getClusterQueue();

if ($undo) {
Expand All @@ -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\"
Expand Down
5 changes: 3 additions & 2 deletions Main/lib/perl/WorkflowSteps/MakeLoadCNVNextflowConfig.pm
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Expand Up @@ -16,15 +16,16 @@ 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");
} else {
open(F, ">", $configPath) or die "$! :Can't open config file '$configPath' for writing";

print F
"
"$sharedClusterConfig
params {
input = \"$input\"
outputDir = \"$outputDir\"
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeLongReadRnaSeqNextflowConfig.pm
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Expand Up @@ -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";
Expand All @@ -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\"
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeMassSpecNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -64,7 +65,7 @@ includeConfig "$clusterConfigFile"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
3 changes: 2 additions & 1 deletion Main/lib/perl/WorkflowSteps/MakeNgsSamplesNextflowConfig.pm
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Expand Up @@ -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";
Expand Down Expand Up @@ -100,7 +101,7 @@ workDir = "$digestedAnalysisDirPath/ngs-samples-work"

NEXTFLOW

print F $configString . $lsfEnv;
print F $sharedClusterConfig . $configString . $lsfEnv;
close(F);
}
}
Expand Down
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