Merge pull request #91 from apeltzer/master

Fix Github Actions tests

.github/workflows/main.yml

@@ -1,9 +1,19 @@
 name: Configs tests
 
+on: [pull_request, push]
 jobs:
+  test_all_profiles:
+    runs-on: ubuntu-latest
+    name: Check if all profiles are tested
+    steps:
+      - uses: actions/checkout@v1
+      - name: Check whether profiles are all tested
+        run: | 
+          python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
   profile_test:
     runs-on: ubuntu-latest
-    name: Run individual profiles
+    name: Run ${{ matrix.profile }} profile
+    needs: test_all_profiles
     strategy:
         matrix:
             profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'czbiohub_aws_highpriority', 'czbiohub_aws', 'denbi_qbic', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh']
@@ -13,8 +23,7 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      - name: Check whether profiles are all tested
-        run: | 
-          python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
-      - name: "Check profile"
-        run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
+      - name: Check ${{ matrix.profile }} profile
+        env: 
+          SCRATCH: '~'
+        run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

conf/prince.config

@@ -18,10 +18,6 @@ singularity {
 }
 
 process {
-        beforeScript = """
-                          module load $singularityModule 
-                          module load $squashfsModule 
-                       """
-                       .stripIndent()
+        beforeScript = "module load $singularityModule $squashfsModule"
         executor = 'slurm'
 }