diff --git a/demo.py b/demo.py index ea34bfb..2b8dbd5 100644 --- a/demo.py +++ b/demo.py @@ -46,7 +46,7 @@ def synstage_info(self, samplesheet_uri: str) -> LaunchInfo: run_name=run_name, pipeline="Sage-Bionetworks-Workflows/nf-synapse", revision="main", - profiles=["sage"], + profiles=["docker"], entry_name="NF_SYNSTAGE", params={ "input": samplesheet_uri, @@ -125,13 +125,13 @@ class TowerRnaseqFlow(FlowSpec): help="S3 prefix for storing output files from different runs", ) - def get_staged_samplesheet(self, samplesheet: str) -> str: + def get_staged_samplesheet(self, samplesheet: str, run_name: str) -> str: """Generate staged samplesheet based on synstage behavior.""" scheme, _, samplesheet_resource = samplesheet.partition("://") if scheme != "s3": raise ValueError("Expected an S3 URI.") path = PurePosixPath(samplesheet_resource) - return f"{scheme}://{path.parent}/{path.name}" + return f"{scheme}://{path.parent}/synstage/{run_name}/{path.name}" def monitor_workflow(self, workflow_id): """Monitor any workflow run (wait until done).""" @@ -186,7 +186,7 @@ def monitor_synstage(self): @step def launch_rnaseq(self): """Launch nf-core/rnaseq workflow to process RNA-seq data.""" - staged_uri = self.get_staged_samplesheet(self.samplesheet_uri) + staged_uri = self.get_staged_samplesheet(self.samplesheet_uri, self.dataset.get_run_name("synstage")) launch_info = self.dataset.rnaseq_info(staged_uri, self.rnaseq_outdir) self.rnaseq_id = self.tower.launch_workflow(launch_info, "spot") self.next(self.monitor_rnaseq)