add docker network to nextflow

nadeemlab · Dec 16, 2023 · bece9ef · bece9ef
1 parent 9392d7a
commit bece9ef
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Showing 4 changed files with 11 additions and 4 deletions.
diff --git a/build/workflow/Makefile b/build/workflow/Makefile
@@ -101,7 +101,7 @@ ${STANDALONE_MODULE_TEST}: ${MODULE_TESTS}
     if [[ "$$extension" == "py" ]]; then executor=python; fi ; \
     if [[ "$$extension" == "sh" ]]; then executor=bash; fi ; \
     cd ../../${TEST_LOCATION}/${MODULE_NAME}/ ; \
-    $$executor $$filename; \
+    $$executor $$filename ${DOCKER_ORG_NAME}-development/${DOCKER_REPO_PREFIX}-development:latest ; \
     echo "$$?" > status_code
 >@${MESSAGE} end "Passed." "Failed."
 >@rm -f status_code

diff --git a/spatialprofilingtoolbox/workflow/assets/nextflow.config.jinja b/spatialprofilingtoolbox/workflow/assets/nextflow.config.jinja
@@ -95,3 +95,9 @@ env.cuda_ = '{{ cuda }}'{% endif %}
 
 {%- if random_seed is defined %}
 env.random_seed_ = '{{ random_seed }}'{% endif %}
+
+{%- if workflow == 'cggnn' and network is not none %}
+docker {
+    runOptions = '--network {{ network }}'
+}
+{%- endif %}
diff --git a/test/workflow/module_tests/.workflow.config b/test/workflow/module_tests/.workflow.config
@@ -16,3 +16,4 @@ merge_rois = true
 upload_importances = false
 cuda = false
 random_seed = 0
+network = workflow_isolated_temporary_test
diff --git a/test/workflow/module_tests/no_docker_test_cggnn.sh b/test/workflow/module_tests/no_docker_test_cggnn.sh
@@ -4,8 +4,8 @@ source env/bin/activate
 pip install ../..[workflow]
 
 # Run the workflow
-spt workflow configure --local --workflow='cggnn' --study-name='Melanoma intralesional IL2' --database-config-file=module_tests/.spt_db.config.container --workflow-config-file=module_tests/.workflow.config
-nextflow run . -with-docker
+spt workflow configure --local --workflow='cggnn' --study-name='Melanoma intralesional IL2' --database-config-file=../db/.spt_db.config.container --workflow-config-file=module_tests/.workflow.config
+nextflow run . -with-docker $1
 
 # Check if the workflow ran successfully and if the expected output files exist
 if [ $? -ne 0 ] || [ ! -e "results/model/model_best_validation_accuracy.pt" ] || [ ! -e "results/model/model_best_validation_loss.pt" ] || [ ! -e "results/model/model_best_validation_weighted_f1_score.pt" ] || [ ! -e "results/importances.csv" ] || [ ! -e "results/feature_names.txt" ] || [ ! -e "results/graphs.pkl" ]; then
@@ -68,6 +68,6 @@ else
 fi
 
 # Clean up
-rm -f .nextflow.log*; rm -rf .nextflow/; rm -f configure.sh; rm -f run.sh; rm -f main.nf; rm -f nextflow.config; rm -f top_100_structures.txt; rm -f top_100_reference.txt; rm -rf results/
+rm -f .nextflow.log*; rm -rf .nextflow/; rm -f configure.sh; rm -f run.sh; rm -f main.nf; rm -f nextflow.config; rm -f top_100_structures.txt; rm -f top_100_reference.txt; # rm -rf results/
 deactivate
 rm -rf env/