Update to have astrocyte version and testing. Closes #41.

.gitlab-ci.yml

 before_script:
-  - module load astrocyte
   - module load python/3.6.1-2-anaconda
   - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
   - module load nextflow/20.01.0
@@ -16,6 +15,8 @@ stages:
 astrocyte_check:
   stage: astrocyte
   script:
+    - module unload nextflow
+    - module load astrocyte/0.4.0rc
     - astrocyte_cli check .
   artifacts:
     expire_in: 2 days
@@ -24,6 +25,19 @@ astrocyte_check:
     when:
       - always
 
+simple_astrocyte:
+  stage: astrocyte
+  script:
+    - module unload nextflow
+    - module load astrocyte/0.4.0rc
+    - astrocyte_cli test "$CI_PROJECT_DIR" --param=bcl,"test_data/simple1/*.tar.gz" --param=designFile,"test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --param=ci,true
+  artifacts:
+    expire_in: 2 days
+  retry:
+    max: 0
+    when:
+      - always
+
 simple_1FC:
   stage: simple
   script:

README.md

@@ -2,6 +2,8 @@
 |:-:|:-:|
 |[![Pipeline Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/commits/master)|[![Pipeline Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/badges/develop/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/commits/develop)|
 
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.01.0-26af64)](https://www.nextflow.io/)
+[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.4.0-blue)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2652611.svg)](https://doi.org/10.5281/zenodo.2652611)
 
 10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline