Deprecate Google Cloud configuration JSONs (#711)

.github/workflows/testwdls.yaml

@@ -54,10 +54,7 @@ jobs:
           # Setup for running womtool
           pip install jinja2==3.1.2
           wget -O womtool.jar https://github.com/broadinstitute/cromwell/releases/download/84/womtool-84.jar
-          echo \
-            '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' \
-            > inputs/values/google_cloud.my_project.json
-          scripts/inputs/build_default_inputs.sh -d . -c google_cloud.my_project
+          scripts/inputs/build_default_inputs.sh -d .
 
       - name: Test with Miniwdl
         run: |

README.md

@@ -125,14 +125,6 @@ Example workflow inputs can be found in `/inputs`. Build using `scripts/inputs/b
 generates input jsons in `/inputs/build`. Except the MELT docker image, all required resources are available in public 
 Google buckets. 
 
-Some workflows require a Google Cloud Project ID to be defined in a cloud environment parameter group. Workspace builds 
-require a Terra billing project ID as well. An example is  provided at `/inputs/values/google_cloud.json` but should 
-not be used, as modifying this file will cause tracked changes in the repository. Instead, create a copy in the same 
-directory with the format `google_cloud.my_project.json` and modify as necessary.
-
-Note that these inputs are required only when certain data are located in requester pays buckets. If this does not 
-apply, users may use placeholder values for the cloud configuration and simply delete the inputs manually.
-
 #### MELT
 **Important**: The example input files contain MELT inputs that are NOT public (see [Requirements](#requirements)). These include:
 
@@ -150,8 +142,7 @@ We recommend running the pipeline on a dedicated [Cromwell](https://github.com/b
 > cp $GATK_SV_ROOT/wdl/*.wdl .
 > zip dep.zip *.wdl
 > cd ..
-> echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
-> bash scripts/inputs/build_default_inputs.sh -d $GATK_SV_ROOT -c google_cloud.my_project
+> bash scripts/inputs/build_default_inputs.sh -d $GATK_SV_ROOT
 > cp $GATK_SV_ROOT/inputs/build/ref_panel_1kg/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json GATKSVPipelineBatch.my_run.json
 > cromshell submit wdl/GATKSVPipelineBatch.wdl GATKSVPipelineBatch.my_run.json cromwell_config.json wdl/dep.zip
 ```
@@ -231,14 +222,12 @@ Here is an example of how to generate workflow input jsons from `GATKSVPipelineB
     --final-workflow-outputs-dir gs://my-outputs-bucket \
     metadata.json \
     > inputs/values/my_ref_panel.json
-> # Define your google project id (for Cromwell inputs) and Terra billing project (for workspace inputs)
-> echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
-> # Build test files for batched workflows (google cloud project id required)
+> # Build test files for batched workflows
 > python scripts/inputs/build_inputs.py \
     inputs/values \
     inputs/templates/test \
     inputs/build/my_ref_panel/test \
-    -a '{ "test_batch" : "ref_panel_1kg", "cloud_env": "google_cloud.my_project" }'
+    -a '{ "test_batch" : "ref_panel_1kg" }'
 > # Build test files for the single-sample workflow
 > python scripts/inputs/build_inputs.py \
     inputs/values \

scripts/cromwell/launch_wdl.sh

@@ -15,15 +15,6 @@ done
 WDL_FILENAME=$(basename "$WDL")
 WDL_NAME=${WDL_FILENAME%.*}
 
-CLOUD_ENV="$GATK_SV_ROOT/inputs/values/google_cloud.my_project.json"
-echo "CLOUD_ENV=$CLOUD_ENV"
-cat << EOF > "$CLOUD_ENV"
-{
-  "google_project_id": "broad-dsde-methods",
-  "terra_billing_project_id": "broad-dsde-methods"
-}
-EOF
-
 
 RUN_DIR="$GATK_SV_ROOT/runs/$WDL_NAME"
 DEPS_ZIP="$RUN_DIR/deps.zip"
@@ -34,10 +25,8 @@ zip "$DEPS_ZIP" *.wdl &> /dev/null
 cd "$GATK_SV_ROOT"
 "$GATK_SV_ROOT/scripts/inputs/build_default_inputs.sh" \
   -d "$GATK_SV_ROOT" \
-  -c google_cloud.my_project \
   > /dev/null
 
-rm -f $CLOUD_ENV
 
 echo "Available input jsons:"
 printf "%d\t%s\n" 0 "none (skip cromwell submit)"

scripts/inputs/build_default_inputs.sh

@@ -2,9 +2,8 @@
 
 function usage() {
   printf "Usage: \n \
-    %s -d <REPO_BASE_DIR> -c <CLOUD_ENV> \n \
-    <REPO_BASE_DIR> \t path to gatk-sv base directory \n \
-    <CLOUD_ENV> \t name of cloud environment json (e.g. 'google_cloud.my' for  inputs/values/google_cloud.my.json)" "$1"
+    %s -d <REPO_BASE_DIR> \n \
+    <REPO_BASE_DIR> \t path to gatk-sv base directory" "$1"
 }
 
 if [[ "$#" == 0 ]]; then
@@ -14,10 +13,9 @@ fi
 #################################################
 # Parsing arguments
 #################################################
-while getopts "d:c:" option; do
+while getopts "d:" option; do
   case "$option" in
     d) BASE_DIR="$OPTARG" ;;
-    c) CLOUD_ENV="$OPTARG" ;;
     *) usage "$0" && exit 1 ;;
   esac
 done
@@ -28,12 +26,6 @@ if [ -z "$BASE_DIR" ] ; then
     exit 1
 fi
 
-if [ -z "$CLOUD_ENV" ] ; then
-    echo "xy"
-    usage "$0"
-    exit 1
-fi
-
 if [[ ! -d "$BASE_DIR" ]]; then
    echo "Invalid directory: $BASE_DIR"
    exit 1
@@ -45,17 +37,16 @@ bash scripts/inputs/clean_default_inputs.sh -d ${BASE_DIR}
 
 echo "########## Building ref_panel_1kg test ##########"
 scripts/inputs/build_inputs.py ${BASE_DIR}/inputs/values ${BASE_DIR}/inputs/templates/test ${BASE_DIR}/inputs/build/ref_panel_1kg/test \
-  -a '{ "test_batch" : "ref_panel_1kg", "cloud_env" : "'$CLOUD_ENV'" }'
+  -a '{ "test_batch" : "ref_panel_1kg" }'
 
 echo "########## Building ref_panel_1kg cohort Terra workspace ##########"
 scripts/inputs/build_inputs.py ${BASE_DIR}/inputs/values ${BASE_DIR}/inputs/templates/terra_workspaces/cohort_mode ${BASE_DIR}/inputs/build/ref_panel_1kg/terra \
-  -a '{ "test_batch" : "ref_panel_1kg", "cloud_env" : "'$CLOUD_ENV'" }'
+  -a '{ "test_batch" : "ref_panel_1kg" }'
 
 echo "########## Building hgdp test ##########"
 scripts/inputs/build_inputs.py ${BASE_DIR}/inputs/values ${BASE_DIR}/inputs/templates/test ${BASE_DIR}/inputs/build/hgdp/test \
-  -a '{ "test_batch" : "hgdp", "cloud_env" : "'$CLOUD_ENV'" }'
+  -a '{ "test_batch" : "hgdp" }'
 
-# Note CLOUD_ENV is not currently required for the single-sample workflow
 echo "########## Building NA19240 single-sample test ##########"
 scripts/inputs/build_inputs.py ${BASE_DIR}/inputs/values ${BASE_DIR}/inputs/templates/test/GATKSVPipelineSingleSample ${BASE_DIR}/inputs/build/NA19240/test \
   -a '{ "single_sample" : "test_single_sample_NA19240", "ref_panel" : "ref_panel_1kg" }'

scripts/inputs/build_inputs.py

@@ -117,15 +117,12 @@ def main():
     raw_input_bundles['test_batch_empty']['name'] = 'test_batch'
     raw_input_bundles['single_sample_none'] = {}
     raw_input_bundles['single_sample_none']['name'] = 'single_sample'
-    raw_input_bundles['cloud_env_none'] = {}
-    raw_input_bundles['cloud_env_none']['name'] = 'cloud_env'
 
     default_aliases = {'dockers': 'dockers',
                        'ref_panel': 'ref_panel_empty',
                        'reference_resources': 'resources_hg38',
                        'test_batch': 'test_batch_empty',
-                       'single_sample': 'single_sample_none',
-                       'cloud_env': 'cloud_env_none'}
+                       'single_sample': 'single_sample_none'}
 
     # prepare the input_dict using default, document default, and user-specified aliases
     input_dict = {}

website/docs/advanced/build_inputs.md

@@ -21,20 +21,10 @@ You may run the following commands to get these example inputs.
    git clone https://github.com/broadinstitute/gatk-sv && cd gatk-sv
     ```
 
-2. Create a JSON file containing the Terra billing project (for use on Terra) 
-   or the Google project ID (for use on Cromwell) that you will use to run 
-   the workflows with the test input. You may create this file by running
-   the following command and replacing `"my-google-project-id"` and 
-   `"my-terra-billing-project"` with your project and billing IDs. 
+2. Create test inputs.
 
     ```shell
-    echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
-    ```
-
-3. Create test inputs.
-
-    ```shell
-    bash scripts/inputs/build_default_inputs.sh -d . -c google_cloud.my_project 
+    bash scripts/inputs/build_default_inputs.sh -d .
     ```
 
     Running this command generates test inputs in `gatk-sv/inputs/build` with the following structure. 
@@ -62,7 +52,7 @@ python scripts/inputs/build_inputs.py \
   inputs/values \
   inputs/templates/test/GATKSVPipelineSingleSample \
   inputs/build/NA19240/test \
-  -a '{ "test_batch" : "ref_panel_1kg", "cloud_env": "google_cloud.my_project" }'
+  -a '{ "test_batch" : "ref_panel_1kg" }'
 ```
 
 
@@ -98,24 +88,18 @@ Here is an example of how to generate workflow input jsons from `GATKSVPipelineB
       metadata.json \
       > inputs/values/my_ref_panel.json
    ```
-
-3. Define your google project id (for Cromwell inputs) and Terra billing project (for workspace inputs).
-
-   ```shell
-   echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
-   ```
 
-4. Build test files for batched workflows (google cloud project id required).
+3. Build test files for batched workflows (google cloud project id required).
 
    ```shell
    python scripts/inputs/build_inputs.py \
       inputs/values \
       inputs/templates/test \
       inputs/build/my_ref_panel/test \
-      -a '{ "test_batch" : "ref_panel_1kg", "cloud_env": "google_cloud.my_project" }'
+      -a '{ "test_batch" : "ref_panel_1kg" }'
    ```
 
-5. Build test files for the single-sample workflow
+4. Build test files for the single-sample workflow
 
    ```shell
    python scripts/inputs/build_inputs.py \
@@ -125,7 +109,7 @@ Here is an example of how to generate workflow input jsons from `GATKSVPipelineB
        -a '{ "single_sample" : "test_single_sample_NA19240", "ref_panel" : "my_ref_panel" }'
    ```
 
-6. Build files for a Terra workspace.
+5. Build files for a Terra workspace.
 
    ```shell 
    python scripts/inputs/build_inputs.py \

website/docs/gs/quick_start.md

@@ -44,8 +44,7 @@ The input values are provided only as an example and are not publicly accessible
 > cp $GATK_SV_ROOT/wdl/*.wdl .
 > zip dep.zip *.wdl
 > cd ..
-> echo '{ "google_project_id": "my-google-project-id", "terra_billing_project_id": "my-terra-billing-project" }' > inputs/values/google_cloud.my_project.json
-> bash scripts/inputs/build_default_inputs.sh -d $GATK_SV_ROOT -c google_cloud.my_project
+> bash scripts/inputs/build_default_inputs.sh -d $GATK_SV_ROOT
 > cp $GATK_SV_ROOT/inputs/build/ref_panel_1kg/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json GATKSVPipelineBatch.my_run.json
 > cromshell submit wdl/GATKSVPipelineBatch.wdl GATKSVPipelineBatch.my_run.json cromwell_config.json wdl/dep.zip
 ```