Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Develop testing dx wdl #1

Merged
merged 63 commits into from
Mar 15, 2018
Merged

Develop testing dx wdl #1

merged 63 commits into from
Mar 15, 2018

Conversation

leepc12
Copy link
Contributor

@leepc12 leepc12 commented Mar 15, 2018

Jenkins and dxWDL support

leepc12 and others added 30 commits January 18, 2018 09:28
@leepc12
fix bug (wrong relative path for Dockerfile) in Dockerfile
428cb49
@leepc12
fix bug in atac.wdl (wrong param name for --pval-thresh)
3f6b12e
@leepc12
Added test_atac.wdl and Jenkins test shell script
624f1e3
@leepc12
cromwell test server/sample setup is almost done. still testing...
82821c7
@leepc12
added/tested pipeline testing module (/test)
b5c1f18
@leepc12
added wf_opt json file for testing, fixed typo in TEST.md
2becb2c
@ottojolanki
Make everything on Jenkins run on master for now
011fe4d
@ottojolanki
try to run test_atac.sh
fb494bd
@leepc12
chmod +x for all *.sh for testing
0b39650
@leepc12
Merge branch 'develop_test_jenkins' of https://github.com/ENCODE-DCC/…
8e3ae81 
…atac-seq-pipeline into develop_test_jenkins
@ottojolanki
test
2413783
@ottojolanki
Merge branch 'develop_test_jenkins' of github.com:ENCODE-DCC/atac-seq…
ef24e3b 
…-pipeline into develop_test_jenkins
@ottojolanki
testing cromwell
750cc81
@ottojolanki
Test quay.io log in and log out
caeae44
@ottojolanki
Test quay.io log in and log out
6b97fc8
@ottojolanki
test making the tag dynamically
ea2cb9a
@ottojolanki
test making the tag dynamically
fb9818a
@ottojolanki
Test building the docker image on a slave, and pushing it to quay.io …
166c759 
…as robot user
@ottojolanki
Test image tagging
b147661
@ottojolanki
Test image tagging
ead20d8
@ottojolanki
Test building the docker image on a slave, and pushing it to quay.io …
76dc5cf 
…as robot user v2
@leepc12
updated test module (new task-level and workflow-level tests)
0415216
@leepc12
updated README for test
dea5c18
@ottojolanki
added --single-branch flags to git clone commands
c712591
@ottojolanki
added .dockerignore file
b905766
@ottojolanki
.dockerignore formatting
6a6ea3e
@ottojolanki
modified timestamps
1f33681
@leepc12
bug fix for testing module
3c66d91
@leepc12
update readme, added chr19 only sample to workflow level test
6ac0800
@leepc12
Merge branch 'develop_test_jenkins' of https://github.com/ENCODE-DCC/…
6dc37f5 
…atac-seq-pipeline into develop_test_jenkins
ottojolanki and others added 19 commits February 13, 2018 13:22
@ottojolanki
run several tests
ee21e69
@ottojolanki
parsing results testing
6f759f2
@ottojolanki
run all the task-level tests
43c594d
@ottojolanki
run all the task-level tests
36a3abd
@ottojolanki
correct typo in Jenkinsfile
22ea4b0
@leepc12
testing atac_dx.wdl with dxWDL
e281bca
@leepc12
update README
c4c9be6
@leepc12
Merge branch 'develop_test_jenkins' of https://github.com/ENCODE-DCC/…
cdd0122 
…atac-seq-pipeline into develop_test_jenkins
@ottojolanki
Update data repo location, run workflow tests
bdca1c8
@leepc12
update README
22732d2
@leepc12
Merge branch 'develop_test_jenkins' of https://github.com/ENCODE-DCC/…
f437ca2 
…atac-seq-pipeline into develop_test_jenkins
@ottojolanki
add set -x to test_atac.sh to debug
ebd4693
@ottojolanki
corrected typo, added PE workflow test
113a6b7
@ottojolanki
disable workflow level tests for now
ff3df38
@leepc12
finished dxWDL things
2b53641
@leepc12
split big scatter into pieces for better parallelization
acb0afe
@leepc12
Merge branch 'develop_test_jenkins' into develop_testing_dxWDL
1ab8db9
@leepc12
finished dxWDL
03da42c
@leepc12
fix typo in workflow tester sh
b175307
@leepc12 leepc12 merged commit 0a980e3 into develop_v1 Mar 15, 2018
@leepc12 leepc12 deleted the develop_testing_dxWDL branch March 15, 2018 23:41
This was referenced Nov 5, 2018
Closed
Closed
@jwtobias jwtobias mentioned this pull request Dec 1, 2018
Closed
@yifeisun03 yifeisun03 mentioned this pull request Feb 27, 2019
Closed
@jwtobias jwtobias mentioned this pull request Apr 30, 2019
Closed
leepc12 added a commit that referenced this pull request May 6, 2019
@leepc12
Merge pull request #1 from ENCODE-DCC/hotfix_v1_PIP-333_dx_se_fastq_d…
e36d8be 
…ef_and_reproducibility_idr_opt_arr_err

Hotfix v1 pip 333 dx se fastq def and reproducibility idr opt arr err
@jwtobias jwtobias mentioned this pull request Jun 24, 2019
Closed
@YuhaoDoong YuhaoDoong mentioned this pull request Dec 5, 2019
Closed
@hariiyer16 hariiyer16 mentioned this pull request Jul 6, 2021
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@leepc12 @ottojolanki