use setup_process_afterscript #314
Conversation
sorelfitzgibbon
requested review from
tyamaguchi-ucla,
yashpatel6,
maotian06 and
a team
as code owners
sorelfitzgibbon
removed request for
maotian06,
tyamaguchi-ucla and
yashpatel6
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@sorelfitzgibbon You're running into the same issue as uclahs-cds/pipeline-Nextflow-module#42 - all of our modules have
My fix from uclahs-cds/pipeline-Nextflow-module#42 was to add So to fix this:
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Actually, I'm not sure about this one... those might be right. Maybe those don't need to be reverted. |
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Works now with pipeline-nextflow-module update, commit 9f07b9fee6bcd742ef8f461b62782522bb69f65e |
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/fix-tests |
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Bleep bloop, I am a robot. You requested that I fix the tests, but I can only do so after posting a comment saying that I can do so. |
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Bleep bloop, I am a robot. Alas, some of the Nextflow configuration tests failed! test/configtest-F16.json@ ["process","afterScript"]
+ {"1":"","2":"","3":"","closure":""}
@ ["process","ext"]
+ {"capture_logs":true,"commonAfterScript":{"1":"","2":"","3":"","closure":""},"log_dir":{"1":"ext","2":"ext","3":"ext","closure":"ext"}}test/configtest-F32.json@ ["process","afterScript"]
+ {"1":"","2":"","3":"","closure":""}
@ ["process","ext"]
+ {"capture_logs":true,"commonAfterScript":{"1":"","2":"","3":"","closure":""},"log_dir":{"1":"ext","2":"ext","3":"ext","closure":"ext"}}If the above changes are surprising, stop and determine what happened. If the above changes are expected, there are two ways to fix this:
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/fix-tests |
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Bleep bloop, I am a robot. I have updated all of the failing tests for you with 2d7af58. You must review my work before merging this pull request! |
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Description
Closes #301
Testing Results
cases: a_mini-all-tools-std-input
These extra files are created.
They seem to be duplicates of the same files except including the additional (correct) tool-tool-version directory and the (correct) suffixes on the final directory. e.g.
I haven't been able to identify the reason and wonder if it's happening within the submodule; some kind of a default log being created as well as that specified by
log_output_dirChecklist
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have reviewed the Nextflow pipeline standards.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added my name to the contributors listings in the
manifestblock in thenextflow.configas part of this pull request; I am listed already, or do not wish to be listed. (This acknowledgement is optional.)I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)I have tested the pipeline on at least one A-mini sample.