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Derive the nextflow branch key and URL from the workflow being run #14

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Merged
jbrestel merged 1 commit into from
Sep 9, 2026
Merged

Derive the nextflow branch key and URL from the workflow being run #14

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10 changes: 5 additions & 5 deletions StepClasses/lib/perl/RunAndMonitorNextflow.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,6 @@ sub run {
my $entry = $self->getParamValue("entry");

# TODO: why do we have the boolean param for "isGitRepo?"
$nextflowWorkflow = "https://github.com/".$nextflowWorkflow;

my $isGitRepo = $self->getBooleanParamValue("isGitRepo");

# get global properties
Expand Down Expand Up @@ -115,16 +113,18 @@ sub runAndMonitor {

# default to main branch but take from step shared if defined
# the workflow branch is gotten via lowercase nextflow workflow param + ".branch"
my $nextflowWorkflowBranchKey = $self->getParamValue("nextflowWorkflow") . ".branch";
my $nextflowWorkflowBranchKey = $nextflowWorkflow . ".branch";
my $workflowBranch = $self->getSharedConfigRelaxed($nextflowWorkflowBranchKey) ? $self->getSharedConfigRelaxed($nextflowWorkflowBranchKey) : "main";

my $nextflowWorkflowUrl = "https://github.com/" . $nextflowWorkflow;

#my $nextflowCmd = "nextflow run $nextflowWorkflow -with-trace -c $clusterNextflowConfigFile -resume >$nextflowStdoutFile 2>&1";
#use "-C" instead of "-c" to avoid taking from anything besides the specified config

my $nextflowCmd = "nextflow -log $logFile -C $clusterNextflowConfigFile run $nextflowWorkflow -r $workflowBranch -resume ";
my $nextflowCmd = "nextflow -log $logFile -C $clusterNextflowConfigFile run $nextflowWorkflowUrl -r $workflowBranch -resume ";

if ($entry) {
$nextflowCmd = "nextflow -log $logFile -C $clusterNextflowConfigFile run $nextflowWorkflow -entry $entry -r $workflowBranch -resume";
$nextflowCmd = "nextflow -log $logFile -C $clusterNextflowConfigFile run $nextflowWorkflowUrl -entry $entry -r $workflowBranch -resume";
}

my $submitCmd = $self->getNodeClass()->getQueueSubmitCommand($queue, $nextflowCmd, undef, undef, $nextflowStdoutFile);
Expand Down