Fixes season error in example.

Author: Robert Chu

.gitignore

@@ -127,3 +127,5 @@ terraform.tfvars
 
 # This is autogenerated during CD
 VERSION
+
+.DS_Store

config.json

@@ -10,7 +10,9 @@
         "--threads",
         "8",
         "--season",
-        "$SEASON"
+        "winter",
+        "--skipDownload",
+        "TRUE"
     ],
     "inputs": {
         "path_args": [
@@ -20,12 +22,7 @@
                 "path_regex_match_group": 1
             }
         ],
-        "query_args": [
-            {
-                "env_var_name": "SEASON",
-                "query_var_name": "season"
-            }
-        ],
+        "query_args": [],
         "body_args": []
     },
     "outputs": {

docker-compose.yaml

@@ -21,8 +21,6 @@ services:
       - "CELERY_RESULT_BACKEND=redis://:${REDIS_PASSWORD}@redis:6379"
     ports:
       - 5000:5000
-    volumes:
-      - ./:/app
   worker:
     image: labflow/script-runner-example:latest
     build:
@@ -37,9 +35,6 @@ services:
     environment:
       - "CELERY_BROKER_URL=redis://:${REDIS_PASSWORD}@redis:6379"
       - "CELERY_RESULT_BACKEND=redis://:${REDIS_PASSWORD}@redis:6379"
-      - "COMMAND_RUNDIR_BASE=/base-rundir"
-    volumes:
-      - ./:/app
   redis:
     image: redis:6-alpine
     command: redis-server --requirepass ${REDIS_PASSWORD}

docker/Dockerfile.example

@@ -57,11 +57,11 @@ RUN R --slave -e "BiocManager::install(c('savR', 'edgeR', 'qvalue', 'ShortRead',
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # swabseq-analysis script
 RUN git clone git://github.com/lab-grid/swabseq-analysis /app
+WORKDIR /app
+RUN git checkout 221990c0521b8896fb0cf0bc5668996989bb2ab6
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # Python Env
-WORKDIR /app
-
 RUN pip3 install pandas
 
 COPY . /script-runner