Merge pull request #255 from ENCODE-DCC/WRAN-1863_update_default_genome_tsv_to_v4

Wran 1863 update default genome tsv to v4

Author: leepc12

.circleci/config.yml

@@ -16,16 +16,6 @@ make_tag: &make_tag
     echo "export TAG=encodedcc/chip-seq-pipeline:${CIRCLE_BRANCH}_${CIRCLE_WORKFLOW_ID}" > ${BASH_ENV}
 
 commands:
-  download_task_test_data:
-    description: "Download task test data. This is based on py2 so run this before installing py3."
-    steps:
-      - run:
-          command: |
-            cd dev/test/test_task/
-            rm -rf chip-seq-pipeline-test-data
-            export BOTO_CONFIG=/dev/null
-            gsutil -m cp -r gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/chip-seq-pipeline-test-data .
-
   install_python3_caper_gcs:
     description: "Install py3, caper and gcs. Set py3 as default python."
     steps:      
@@ -86,7 +76,7 @@ jobs:
           name: build image
           command: |
             source ${BASH_ENV}
-            export DOCKER_CACHE_TAG=v1.8.1
+            export DOCKER_CACHE_TAG=v2.1.0
             echo "pulling ${DOCKER_CACHE_TAG}!"
             docker pull encodedcc/chip-seq-pipeline:${DOCKER_CACHE_TAG}
             docker login -u=${DOCKERHUB_USER} -p=${DOCKERHUB_PASS}
@@ -97,7 +87,6 @@ jobs:
     <<: *machine_defaults
     steps:
       - checkout
-      - download_task_test_data
       - install_python3_caper_gcs
       - run: *make_tag
       - run:
@@ -106,6 +95,9 @@ jobs:
             source ${BASH_ENV}
             cd dev/test/test_task/
 
+            echo ${GCLOUD_SERVICE_ACCOUNT_SECRET_JSON} > tmp_secret_key.json
+            export GOOGLE_APPLICATION_CREDENTIALS=$PWD/tmp_secret_key.json
+
             # unittest for wrapper .py
             docker run ${TAG} bash -c "cd /software/chip-seq-pipeline/dev/test/test_py/; pytest -vv"
 

.gitignore

@@ -125,3 +125,5 @@ tmp_db*
 temp_db*
 
 cromwell.out
+cromwell.out.*
+

README.md

@@ -127,8 +127,8 @@ You cannot use these input JSON files directly. Go to the destination directory
 We have a separate project on DNANexus to provide example FASTQs and `genome_tsv` for `hg38` and `mm10` (also chr19-only version of those two. Use chr19-only versions for testing). We recommend to make copies of these directories on your own project.
 
 `genome_tsv`
-- AWS: https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/pipeline-genome-data/genome_tsv/v3
-- Azure: https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/pipeline-genome-data/genome_tsv/v3
+- AWS: https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/pipeline-genome-data/genome_tsv/v4
+- Azure: https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/pipeline-genome-data/genome_tsv/v4
 
 Example FASTQs
 - AWS: https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled

chip.wdl

@@ -7,10 +7,10 @@ struct RuntimeEnvironment {
 }
 
 workflow chip {
-    String pipeline_ver = 'v2.1.2'
+    String pipeline_ver = 'v2.1.3'
 
     meta {
-        version: 'v2.1.2'
+        version: 'v2.1.3'
 
         author: 'Jin wook Lee'
         email: '[email protected]'
@@ -19,8 +19,8 @@ workflow chip {
 
         specification_document: 'https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit?usp=sharing'
 
-        default_docker: 'encodedcc/chip-seq-pipeline:v2.1.2'
-        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.2.sif'
+        default_docker: 'encodedcc/chip-seq-pipeline:v2.1.3'
+        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.3.sif'
         croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v5.json'
 
         parameter_group: {
@@ -71,8 +71,8 @@ workflow chip {
     }
     input {
         # group: runtime_environment
-        String docker = 'encodedcc/chip-seq-pipeline:v2.1.2'
-        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.2.sif'
+        String docker = 'encodedcc/chip-seq-pipeline:v2.1.3'
+        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.3.sif'
         String conda = 'encode-chip-seq-pipeline'
         String conda_macs2 = 'encode-chip-seq-pipeline-macs2'
         String conda_spp = 'encode-chip-seq-pipeline-spp'