Merge pull request #31 from drpatelh/master

Add proper test for --skip_ilastik

.github/workflows/ci.yml

@@ -27,36 +27,14 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
-  parameters:
-    env:
-      NXF_VER: '19.10.0'
-      NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters: [--skip_ilastik]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      #- name: Pull docker image (Cant pull standard single image for this pipeline as we are using individual containers)
-      #  run: |
-      #    docker pull nfcore/imcyto:dev
-      #    docker tag nfcore/imcyto:dev nfcore/imcyto:1.0.0
-      - name: Run pipeline with various options
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
-
   config:
     env:
       NXF_VER: '19.10.0'
       NXF_ANSI_LOG: false
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        config: [test_txt, test_tiff]
+        config: [test_txt, test_tiff, test_skip_ilastik]
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow

conf/test_skip_ilastik.config

@@ -0,0 +1,30 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/imcyto -profile test_skip_ilastik,<docker/singularity>
+ */
+
+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 = 12.h
+
+  // Test input data in *.mcd format and --skip_ilastik parameter
+  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/inputs/20191121_BRAC3438.6f.mcd'
+  metadata = 'https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/inputs/metadata.csv'
+
+  full_stack_cppipe = 'https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/full_stack_preprocessing.cppipe'
+  ilastik_stack_cppipe = 'https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/ilastik_stack_preprocessing.cppipe'
+  segmentation_cppipe = 'https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/segmentation_skip_ilastik.cppipe'
+  ilastik_training_ilp = 'https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/ilastik_training_params.ilp'
+
+  skip_ilastik = true
+}

nextflow.config

@@ -68,9 +68,10 @@ profiles {
     singularity.enabled = true
     singularity.autoMounts = true
   }
-  test      { includeConfig 'conf/test.config' }
-  test_txt  { includeConfig 'conf/test_txt.config' }
-  test_tiff { includeConfig 'conf/test_tiff.config' }
+  test              { includeConfig 'conf/test.config'              }
+  test_txt          { includeConfig 'conf/test_txt.config'          }
+  test_tiff         { includeConfig 'conf/test_tiff.config'         }
+  test_skip_ilastik { includeConfig 'conf/test_skip_ilastik.config' }
 }
 
 // Export this variable to prevent local Python libraries from conflicting with those in the container