Implement caching of test data in github action

.github/workflows/ci.yml

@@ -36,6 +36,35 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: ${{ steps.hash_workspace.outputs.digest }}
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: circrna
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/circrna/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets

conf/test_cache.config

@@ -0,0 +1,34 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/circrna -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 6.h
+
+    // Input data for test data
+    input = "${params.test_data_base}/samples.csv"
+    fasta = "${params.test_data_base}/reference/chrI.fa"
+    gtf = "${params.test_data_base}/reference/chrI.gtf"
+    mature = "${params.test_data_base}/reference/mature.fa"
+    tool = "circexplorer2"
+    phenotype = "${params.test_data_base}/phenotype.csv"
+    skip_trimming = false
+    module = "circrna_discovery,mirna_prediction,differential_expression"
+    outdir = "results/"
+    bsj_reads = 2
+    species = "cel"
+}