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

Fix partitioning in ImportGenome WDL #6939

Merged
merged 1 commit into from
Nov 5, 2020
Merged

Fix partitioning in ImportGenome WDL #6939

merged 1 commit into from
Nov 5, 2020

Conversation

meganshand
Copy link
Contributor

I'm not sure how this worked before, but adding a variable fixes it. @ahaessly, let me know what you think!

@meganshand meganshand requested a review from ahaessly November 4, 2020 18:05
ahaessly
ahaessly approved these changes Nov 4, 2020
View reviewed changes
Copy link
Contributor

@ahaessly ahaessly left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

that is weird. unless "set -e" has a return code. that would overwrite the one from bq show.
maybe used to have the "set -e" inside the if block. that must be it.

but looks good. thanks for fixing!

kcibul
kcibul approved these changes Nov 4, 2020
View reviewed changes
scripts/variantstore_wdl/ImportArrays.wdl
set -e
if [ $? -ne 0 ]; then
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think previously this $? was checking the exit code of set -e (the previous command)... not sure how that ever worked?! your variable is much more clear anyway

@meganshand
Copy link
Contributor Author

Yeah, maybe the environment matters (as to whether or not set -e has a return code)?

@gatk-bot
Copy link

gatk-bot commented Nov 4, 2020

Travis reported job failures from build 32042
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk8 32042.1 logs

@meganshand meganshand merged commit 39dbb1a into ah_var_store Nov 5, 2020
@meganshand meganshand deleted the ms_partition branch November 5, 2020 15:59
kcibul pushed a commit that referenced this pull request Jan 29, 2021
@meganshand @kcibul
fix partitioning (#6939)
b777a1a
kcibul pushed a commit that referenced this pull request Feb 1, 2021
@meganshand @kcibul
fix partitioning (#6939)
0f3fa74
Marianie-Simeon pushed a commit that referenced this pull request Feb 16, 2021
@meganshand
fix partitioning (#6939)
30ac234
kcibul pushed a commit that referenced this pull request Mar 9, 2021
@meganshand @kcibul
fix partitioning (#6939)
31553aa
mmorgantaylor pushed a commit that referenced this pull request Apr 6, 2021
@meganshand @mmorgantaylor
fix partitioning (#6939)
c3d625b
mmorgantaylor pushed a commit that referenced this pull request Apr 6, 2021
@meganshand @mmorgantaylor
fix partitioning (#6939)
3f18f51
This was referenced Mar 17, 2023
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@kcibul kcibul kcibul approved these changes

@ahaessly ahaessly ahaessly approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@meganshand @gatk-bot @kcibul @ahaessly