Fix for permission errors with biocontainer non-root user usage

nextflow-io/nextflow#1295
alliance-genome · Apr 4, 2024 · d89186f · d89186f
1 parent a4cf847
commit d89186f
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diff --git a/pipeline/alignment/Dockerfile b/pipeline/alignment/Dockerfile
@@ -1,3 +1,4 @@
 FROM biocontainers/clustalo:v1.2.4-2-deb_cv1
 
+USER root
 CMD [ "clustalo", "--help" ]
diff --git a/pipeline/workflow/Makefile b/pipeline/workflow/Makefile
@@ -10,9 +10,6 @@ build-workflow-local-deps:
 	make -C ../seq_retrieval/ container-image
 	make -C ../alignment/ container-image
 
-pipeline-results/:
-	mkdir pipeline-results/
-
-run-integration-test: nextflow pipeline-results/
+run-integration-test: nextflow
 	./nextflow run -profile test protein-msa.nf
 	@diff -qs pipeline-results/alignment-output.aln tests/resources/integration-test-results.aln