Infer oncoanalyser output subdirectory from base pipeline directory - Githubissues

umccr / nextflow-stack

AWS stack to run Nextflow pipelines on Batch using shared resources

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Infer oncoanalyser output subdirectory from base pipeline directory #69

Closed scwatts closed 1 year ago

scwatts commented 1 year ago

Background

the portal orchestrator is only aware of the base oncoanalyser pipeline output directory
however, the Nextflow stack currently expects the subdirectory containing only oncoanalyser outputs, e.g.:

Expected: s3://umccr-temp-dev/SBJ00001/oncoanalyser/202310207abcdefg/wgs/L2300001__L2300002/SBJ00001_MDX230001/
Provided: s3://umccr-temp-dev/SBJ00001/oncoanalyser/202310207abcdefg/wgs/L2300001__L2300002/

since the portal orchestrator is not directly given info wrt the required subdir, this difference should be resolved here

Changes

required input directory inferred from base oncoanalyser pipeline output directory
additionally, enforced trailing slashes on directories present in the sash samplesheet

scwatts commented 1 year ago

I've deployed in dev and tested Lambdas Functions along with pipeline execution on EC2 instances using corresponding run commands.