add test

.github/workflows/ci.yml

@@ -42,23 +42,17 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-        #- name: Run pipeline with test data
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
-        #run: |
-        #  nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-      - name: Run pipeline with cBioPortal data
+      - name: Run pipeline with test data
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_cbioportal,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
-        #- name: Run pipeline with COSMIC Cell Lines data
-        #env:
-        #  COSMIC_USERNAME: ${{ secrets.COSMIC_USERNAME }}
-        #  COSMIC_PASSWORD: ${{ secrets.COSMIC_PASSWORD }}
+      - name: Run pipeline with COSMIC Cell Lines and cBioPortal data
+        env:
+          COSMIC_USERNAME: ${{ secrets.COSMIC_USERNAME }}
+          COSMIC_PASSWORD: ${{ secrets.COSMIC_PASSWORD }}
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
-        #run: |
-        #  nextflow run ${GITHUB_WORKSPACE} -profile test_cosmic,docker --outdir ./results --cosmic_user_name $COSMIC_USERNAME --cosmic_password $COSMIC_PASSWORD
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_cosmic_cbio,docker --outdir ./results --cosmic_user_name $COSMIC_USERNAME --cosmic_password $COSMIC_PASSWORD

conf/test_cosmic.config → conf/test_cosmic_cbio.config

@@ -12,7 +12,7 @@
 
 params {
     config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test COSMIC Cell lines generation'
+    config_profile_description = 'Full test COSMIC Cell lines and cBioPortal generation'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
@@ -26,6 +26,6 @@ params {
     gnomad = false
     cosmic = false
     cosmic_celllines = true
-    cbioportal = false
+    cbioportal = true
     decoy = true
 }

conf/test_full.config

@@ -15,9 +15,9 @@ params {
     config_profile_description = 'Full test COSMIC generation'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus = 2
-    max_memory = 6.GB
-    max_time = 48.h
+    //max_cpus = 2
+    //max_memory = 6.GB
+    //max_time = 48.h
 
     // Input data for full size test
     ensembl_name = 'homo_sapiens'

nextflow.config

@@ -184,8 +184,7 @@ profiles {
     }
     test { includeConfig 'conf/test.config' }
     test_full { includeConfig 'conf/test_full.config'      }
-    test_cosmic { includeConfig 'conf/test_cosmic.config' }
-    test_cbioportal { includeConfig 'conf/test_cbioportal.config' }
+    test_cosmic_cbio { includeConfig 'conf/test_cosmic_cbio.config' }
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container