provenance creation for snakemake and nextflow workflows

Author: dtyagi

.github/workflows/run-benchmark.yml

@@ -73,11 +73,32 @@ jobs:
             name: fenics-output
             path: |
               benchmarks/linear-elastic-plate-with-hole/FEniCS/data
-      
+
+      - name: Archive fenics snakemake provenance
+        uses: actions/upload-artifact@v4
+        with:
+            name: fenics-snakemake-provenance
+            path: |
+              benchmarks/linear-elastic-plate-with-hole/FEniCS/*.zip
+
       - name: Archive kratos data
         uses: actions/upload-artifact@v4
         with:
             name: kratos-output
             path: |
               benchmarks/linear-elastic-plate-with-hole/Kratos/data
-              
+
+      - name: Archive fenics nextflow data
+        uses: actions/upload-artifact@v4
+        with:
+            name: fenics-nextflow-output
+            path: |
+              benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/work/**
+              !benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/work/conda/**
+
+      - name: Archive fenics nextflow provenance
+        uses: actions/upload-artifact@v4
+        with:
+            name: fenics-nextflow-provenance
+            path: |
+              benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/provenance.json

benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/nextflow.config

@@ -14,7 +14,7 @@ prov {
   enabled = true
   formats {
     legacy {
-      file = 'provenance.json'
+      file = "provenance.json"
       overwrite = true
     }
   }

environment_benchmarks.yml

@@ -9,3 +9,6 @@ dependencies:
   - meshio
   - conda-lock
   - conda
+  - pip
+  - pip:
+    - git+https://github.com/izus-fokus/snakemake-report-plugin-metadata4ing