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Allow running pipelines from repository subfolders #6602

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2 changes: 1 addition & 1 deletion modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -630,7 +630,7 @@ class CmdRun extends CmdBase implements HubOptions {
/*
* try to look for a pipeline in the repository
*/
def manager = new AssetManager(pipelineName, this)
def manager = new AssetManager(pipelineName, mainScript, this)
def repo = manager.getProject()

boolean checkForUpdate = true
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16 changes: 14 additions & 2 deletions modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
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Expand Up @@ -106,6 +106,14 @@ class AssetManager {
build(pipelineName, config, cliOpts)
}

AssetManager( String pipelineName, String scriptFile, HubOptions cliOpts = null) {
assert pipelineName
// read the default config file (if available)
def config = ProviderConfig.getDefault()
// build the object
build(pipelineName, config, cliOpts, scriptFile)
}

AssetManager( String pipelineName, Map config ) {
assert pipelineName
// build the object
Expand All @@ -121,10 +129,11 @@ class AssetManager {
* @return The {@link AssetManager} object itself
*/
@PackageScope
AssetManager build( String pipelineName, Map config = null, HubOptions cliOpts = null ) {
AssetManager build( String pipelineName, Map config = null, HubOptions cliOpts = null, String scriptFile = null) {

this.providerConfigs = ProviderConfig.createFromMap(config)

if( scriptFile )
this.mainScript = scriptFile
this.project = resolveName(pipelineName)
this.localPath = checkProjectDir(project)
this.hub = checkHubProvider(cliOpts)
Expand Down Expand Up @@ -311,6 +320,9 @@ class AssetManager {
if( !isUrl )
return null

if( repository.endsWith('.nf') || repository.endsWith('.nxf') )
throw new AbortOperationException("Repository URL can end as a script file (.nf|.nxf) - Use -main-script option.")

try {
def url = new GitUrl(repository)

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