Skip to content

Ensure main script is the first one in the lineage WorkflowRun record #6845

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bentsherman merged 3 commits into from
Feb 26, 2026
+6 −6
Merged

Ensure main script is the first one in the lineage WorkflowRun record #6845

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
da3621c
Ensure main script is the first one in the lineage WorkflowRun record
jorgee Feb 19, 2026
fe18e5a
Update documentation in Workflow.groovy
bentsherman Feb 26, 2026
3ff02e1
Merge branch 'master' into fix-main-nf-lineage-workflow-run
bentsherman Feb 26, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions modules/nf-lineage/src/main/nextflow/lineage/LinObserver.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ class LinObserver implements TraceObserverV2 {
}

protected List<DataPath> collectScriptDataPaths(PathNormalizer normalizer) {
final allScripts = allScriptFiles()
final allScripts = allScriptFiles().sort()
final result = new ArrayList<DataPath>(allScripts.size()+1)
// the main script
result.add( new DataPath(
Expand All @@ -148,7 +148,7 @@ class LinObserver implements TraceObserverV2 {
final dataPath = new DataPath(normalizer.normalizePath(it.normalize()), Checksum.ofNextflow(it.text))
result.add(dataPath)
}
return result.sort{it.path}
return result
}

protected String storeWorkflowRun(PathNormalizer normalizer) {
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-lineage/src/main/nextflow/lineage/model/v1beta1/Workflow.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ import nextflow.lineage.serde.LinSerializable
@CompileStatic
class Workflow implements LinSerializable {
/**
* List of script files defining a workflow
* List of script files used by a workflow, starting with the main script
*/
List<DataPath> scriptFiles
/**
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-lineage/src/test/nextflow/lineage/LinObserverTest.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -114,8 +114,8 @@ class LinObserverTest extends Specification {
def store = new DefaultLinStore();
def uniqueId = UUID.randomUUID()
def scriptFile = folder.resolve("main.nf")
def module1 = folder.resolve("script1.nf"); module1.text = 'hola'
def module2 = folder.resolve("script2.nf"); module2.text = 'world'
def module1 = folder.resolve("a_script1.nf"); module1.text = 'hola'
def module2 = folder.resolve("b_script2.nf"); module2.text = 'world'
and:

def metadata = Mock(WorkflowMetadata){
Expand All @@ -139,7 +139,7 @@ class LinObserverTest extends Specification {
when:
def files = observer.collectScriptDataPaths(new PathNormalizer(metadata))
then:
observer.allScriptFiles() >> [ scriptFile, module1, module2 ]
observer.allScriptFiles() >> [ module2, scriptFile, module1 ]
and:
files.size() == 3
and:
Expand Down
Loading