Update workflow

.github/workflows/docker-build-test.yml

@@ -18,4 +18,4 @@ jobs:
     - name: Build docker image
       run: docker build -t test-arcas-hla -f Docker/Dockerfile .
     - name: Test with pytest
-      run: docker run --rm -v $GITHUB_WORKSPACE:/home test-arcas-hla pytest
+      run: docker run --rm -v $GITHUB_WORKSPACE:/app test-arcas-hla pytest

Docker/README.md

@@ -1,20 +1,6 @@
 # Container for arcasHLA #
 
-Installs up-to-date versions of arcasHLA and all dependencies:
-
-- arcasHLA
-- [Git Large File Storage](https://github.com/git-lfs/git-lfs/wiki/Installation)
-- coreutils
-- [Samtools v1.19](http://www.htslib.org/)
-- [bedtools v2.29.1](http://bedtools.readthedocs.io/)
-- [pigz v2.3.1](https://zlib.net/pigz/)
-- [Kallisto v0.44.0](https://pachterlab.github.io/kallisto/)
-- python 3.6
-- [Biopython v1.77](https://biopython.org/wiki/Download)
-- numpy
-- scipy
-- pandas
-- pytest
+Installs up-to-date versions of arcasHLA and all dependencies from `environment.yml`.
 
 ### Build ###
 In order to use this arcasHLA container, install Docker and build in this directory:
@@ -33,5 +19,4 @@ docker run \
 	<image_name> \
 	arcasHLA extract --o docker/path/to/files/out_dir \
 	[other options] docker/path/to/files/sample.bam & 
-
 ```

README.md

@@ -19,7 +19,7 @@ conda activate arcas-hla
 
 ```
 docker build -t <image-name> -f Docker/Dockerfile .
-docker run --rm -v /path/to/repo:/home <image-name> pytest
+docker run --rm -v /path/to/repo:/app <image-name> pytest
 ```
 -----