Merge pull request #176 from ENCODE-DCC/dev

v1.5.1

Author: leepc12

.circleci/config.yml

@@ -48,7 +48,7 @@ commands:
             export GOOGLE_APPLICATION_CREDENTIALS=$PWD/tmp_secret_key.json
             caper run ../../../chip.wdl \
               --backend gcp --gcp-prj ${GOOGLE_PROJECT_ID} \
-              --backend-file backend_gcp_service_account.conf \
+              --gcp-service-account-key-json $PWD/tmp_secret_key.json \
               --out-gcs-bucket ${CAPER_OUT_DIR} --tmp-gcs-bucket ${CAPER_TMP_DIR} \
               -i ${INPUT} -m metadata.json --docker ${TAG}
 
@@ -252,3 +252,4 @@ workflows:
       - test_workflow_hist_pe:
           requires:
             - build
+

README.md

@@ -14,15 +14,15 @@ This ChIP-Seq pipeline is based off the ENCODE (phase-3) transcription factor an
 ## Installation
 
 1) Git clone this pipeline.
-	> **IMPORTANT*: use `~/chip-seq-pipeline2/chip.wdl` as `[WDL]` in Caper's documentation.
+	> **IMPORTANT**: use `~/chip-seq-pipeline2/chip.wdl` as `[WDL]` in Caper's documentation.
 
 	```bash
 	$ cd
 	$ git clone https://github.com/ENCODE-DCC/chip-seq-pipeline2
 	```
 
 2) Install pipeline's [Conda environment](docs/install_conda.md) if you want to use Conda instead of Docker/Singularity. Conda is recommneded on local computer and HPCs (e.g. Stanford Sherlock/SCG). Use 
-	> **IMPORTANT*: use `encode-chip-seq-pipeline` as `[PIPELINE_CONDA_ENV]` in Caper's documentation.
+	> **IMPORTANT**: use `encode-chip-seq-pipeline` as `[PIPELINE_CONDA_ENV]` in Caper's documentation.
 
 3) **Skip this step if you have installed pipeline's Conda environment**. Caper is already included in the Conda environment. [Install Caper](https://github.com/ENCODE-DCC/caper#installation). Caper is a python wrapper for [Cromwell](https://github.com/broadinstitute/cromwell).