Merge pull request #30 from 4dn-dcic/dev

Dev

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 sudo: false
-python: 2.7
+python: 3.6
 os: linux
 services: docker
 addons:
@@ -12,23 +12,12 @@ matrix:
     - env:
         - CWL_TEST_V1=1 CWL_NAME_LIST="hi-c-processing-pairs hi-c-processing-bam pairs-patch addfragtopairs pairsam-filter pairsam-markasdup merge-pairs pairsam-merge pairsam-parse-sort extract-mcool-normvector-for-juicebox md5 fastqc-0-11-4-1 cool2mcool bwa-mem md5-validate"
       install:
-        - pip install git+https://github.com/common-workflow-language/cwltool.git  # for v1
-      script:
-        - set -e;
-          for CWL_NAME in $CWL_NAME_LIST; do
-             source tests/tests_v1.sh $CWL_NAME;
-          done;
-          set +e;
-    - env:
-        - CWL_TEST_DRAFT3=1 CWL_NAME_LIST="hi-c-processing-pairs hi-c-processing-bam pairs-patch addfragtopairs pairsam-filter pairsam-markasdup merge-pairs pairsam-merge pairsam-parse-sort extract-mcool-normvector-for-juicebox md5 fastqc-0-11-4-1 cool2mcool bwa-mem md5-validate"
-      before_install:
         - pip install schema_salad
-      install:
-        - pip install git+https://github.com/SooLee/cwltool.git  # cwltool, for draft-3
+        - pip install cwltool==1.0.20181201184214 # for v1
       script:
         - set -e;
           for CWL_NAME in $CWL_NAME_LIST; do
-             source tests/tests.sh $CWL_NAME;
+             source tests/tests_v1.sh $CWL_NAME;
           done;
           set +e;
     - env:

README.md

@@ -1,5 +1,5 @@
 # pipelines-cwl
-* This is a collection of pipelines built by 4DN-DCIC that were created and run either on the SevenBridges platform or on the 4DN platform, AWSEM.
+* This is a collection of pipelines built by 4DN-DCIC that were used to process 4DN data on the 4DN portal using Tibanna workflow executor.
 
 ### Directories
 * `cwl_awsem` : AWSEM CWLs in draft-3 in json format
@@ -42,16 +42,15 @@ To run docker through CWL, you need a cwl executor - we use `cwltool` (https://g
 
 
 ### Testing CWL
-To test cwls in this repo against the test files in `tests`, use `tests/tests.sh` with cwl name (without .cwl).
+To test cwls in this repo against the test files in `tests`, use `tests/tests_v1.sh` with cwl name (without .cwl).
 ```bash
-source tests/tests.sh bwa-mem
+source tests/tests_v1.sh bwa-mem
 ```
 
-### Benchmark (calculating CPU, Memory, space and determining an instance type)
-The Benchmark is now moved to https://github.com/SooLee/Benchmark
+### Notes on releases
 
-
-### Notes on SBG/AWSEM
+#### Freeze >= 0.2.6
+* All CWL is converted to version 1 (no more draft3) and they are kept in the folder `cwl_awsem_v1`.
 
 #### Freeze >=0.0.2
 * Directory `cwl_awsem` is manually updated starting from freeze 0.0.2 (after Sep 1, 2017), since we no longer use SevenBridges.