Fix ci.yml

.gitignore

@@ -99,7 +99,8 @@ ENV/
 .mypy_cache/
 
 # nextflow analysis folders/files
-/test_data/*
+/test_data/*.fastq.gz
+/test_data/*.fastq
 /workflow/.nextflow/*
 /workflow/work/*
 /workflow/output/*

.gitlab-ci.yml

 before_script:
   - module load python/3.6.1-2-anaconda
   - module load nextflow/0.27.6
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_mkfastq/*tar.gz test_data/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/*fastq.gz test_data/
 
 stages:
   - integration

test_data/design.csv

+Sample,fastq_R1,fastq_R2
+D17PrPzF_BE,D17PrPzF_BE_S1_L001_R1_001.fastq.gz,D17PrPzF_BE_S1_L001_R2_001.fastq.gz
+D17PrPzF_BE,D17PrPzF_BE_S1_L002_R1_001.fastq.gz,D17PrPzF_BE_S1_L002_R2_001.fastq.gz
+D17PrPzF_LE,D17PrPzF_LE_S3_L001_R1_001.fastq.gz,D17PrPzF_LE_S3_L001_R2_001.fastq.gz
\ No newline at end of file