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support for nf-core workflows #4

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support for nf-core workflows #4

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4be8eb7
wip: attempt to support nf-core workflows
d-callan May 2, 2024
f73ea72
add nfcore params file arg
d-callan May 3, 2024
9141024
allow versioning of nf-core pipelines
d-callan May 3, 2024
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40 changes: 32 additions & 8 deletions StepClasses/lib/perl/RunAndMonitorNextflow.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,25 @@ sub getConfigDeclaration {
}

sub runAndMonitor {
my ($self, $test, $user, $submitServer, $transferServer, $jobInfoFile, $logFile, $nextflowStdoutFile, $workingDir, $time, $queue, $nextflowWorkflow, $isGit, $clusterNextflowConfigFile) = @_;
my (
$self,
$test,
$user,
$submitServer,
$transferServer,
$jobInfoFile,
$logFile,
$nextflowStdoutFile,
$workingDir,
$time,
$queue,
$nextflowWorkflow,
$isGit,
$clusterNextflowConfigFile,
$clusterNextflowParamsFile,
$isNfCoreWorkflow,
$pipelineVersion,
) = @_;

if ($self->getSharedConfigRelaxed('masterWorkflowDataDir')) {
$self->log("Skipping runAndMonitorNextflow -- slave workflows don't run nextflow");
Expand All @@ -92,15 +110,21 @@ sub runAndMonitor {
# first see if by any chance we are already done (would happen if somehow the flow lost track of the job)
return 1 if $self->_checkClusterTaskLogForDone($logFile, $user, $transferServer);

#my $nextflowCmd = "nextflow run $nextflowWorkflow -with-trace -c $clusterNextflowConfigFile -resume >$nextflowStdoutFile 2>&1";
my $nextflowCmd = "nextflow"
if ($isNfCoreWorkflow) {
# here we want to inherit config from nf-core, and cant guarantee the default branch is 'main'
$nextflowCmd = "$nextflowCmd -c $clusterNextflowConfigFile run $nextflowWorkflow -with-trace -r $pipelineVersion -params-file $clusterNextflowParamsFile -resume >$nextflowStdoutFile 2>&1";
} else {
#use "-C" instead of "-c" to avoid taking from anything besides the specified config
my $nextflowCmd = "nextflow -C $clusterNextflowConfigFile run $nextflowWorkflow -with-trace -r main -resume >$nextflowStdoutFile 2>&1";
if($isGit){
$nextflowCmd = "nextflow pull $nextflowWorkflow; $nextflowCmd";
}
$nextflowCmd = "$nextflowCmd -C $clusterNextflowConfigFile run $nextflowWorkflow -with-trace -r main -resume >$nextflowStdoutFile 2>&1";
}

if($isGit || $isNfCoreWorkflow) {
$nextflowCmd = "nextflow pull $nextflowWorkflow; $nextflowCmd";
}

# prepend slash to ;, >, and & so that the command is submitted whole
$nextflowCmd =~ s{([;>&])}{\\$1}g;
# prepend slash to ;, >, and & so that the command is submitted whole
$nextflowCmd =~ s{([;>&])}{\\$1}g;

my $submitCmd = $self->getNodeClass()->getQueueSubmitCommand($queue, $nextflowCmd);

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