Merge pull request #19 from CCBR/ci

test: update stub config to make sure cruise init works

.github/workflows/build.yml

@@ -32,4 +32,6 @@ jobs:
           pip install .[dev,test]
       - name: Test stub run
         run: |
+          cd tests/
+          cruise init
           cruise run -profile ci_stub -stub

conf/ci_stub.config

@@ -2,10 +2,10 @@ params {
     config_profile_name = 'Test single-end stubs'
     config_profile_description = 'Minimal test dataset with blank references to run stubs with continuous integration'
 
-    input = 'tests/assets/samplesheet.csv' // adapted from https://github.com/nf-core/test-datasets/blob/chipseq/samplesheet/v2.0/samplesheet_test.csv
+    input = 'assets/samplesheet.csv' // adapted from https://github.com/nf-core/test-datasets/blob/chipseq/samplesheet/v2.0/samplesheet_test.csv
     library = 'assets/lib/yusa_library.csv'
     outdir = 'results/test'
-    design_matrix = 'tests/data/designmat.txt'
+    design_matrix = 'data/designmat.txt'
 
     max_cpus = 2        // for GitHub Actions https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     max_memory = '6.GB'

tests/assets/samplesheet.csv

@@ -1,3 +1,3 @@
 sample,fastq_1,fastq_2,treat_or_ctrl
-s1_rep1,tests/data/file1.fastq.gz,,treatment
-s2_rep1,tests/data/file2.fastq.gz,,control
+s1_rep1,data/file1.fastq.gz,,treatment
+s2_rep1,data/file2.fastq.gz,,control