Merge pull request #165 from ewels/fix-show-profiles

Set params.custom_config_base in nextflow.config

.github/workflows/main.yml

@@ -1,15 +1,28 @@
 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
+
+  check_nextflow_config:
+    runs-on: ubuntu-latest
+    name: Check if nextflow config runs in repository root
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
         run: |
-          python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - run: nextflow config -show-profiles ${GITHUB_WORKSPACE}
+
   profile_test:
     runs-on: ubuntu-latest
     name: Run ${{ matrix.profile }} profile
@@ -82,4 +95,4 @@ jobs:
         env:
           SCRATCH: "~"
           NXF_GLOBAL_CONFIG: awsbatch.config
-        run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
+        run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf -profile ${{ matrix.profile }}

conf/prince.config

@@ -1,6 +1,6 @@
-singularityDir = "$SCRATCH/singularity_images_nextflow"
+def singularityDir = set_singularity_path()
-singularityModule = "singularity/3.2.1"
+def singularityModule = "singularity/3.2.1"
-squashfsModule = "squashfs/4.3"
+def squashfsModule = "squashfs/4.3"
 
 params {
     config_profile_description = """
@@ -21,3 +21,13 @@ process {
         beforeScript = "module load $singularityModule $squashfsModule"
         executor = 'slurm'
 }
+
+def set_singularity_path() {
+    def scratch = System.getenv('SCRATCH')
+    if(scratch == null){
+        System.err.println("WARNING: prince.config requires the SCRATCH env var to be set.")
+        return null
+    } else {
+        return "$SCRATCH/singularity_images_nextflow"
+    }
+}

nextflow.config

@@ -1 +1,2 @@
+params.custom_config_base = "."
 includeConfig("nfcore_custom.config")