Process afterscript #164
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Process afterscript #164
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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"}}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 30c7296. You must review my work before merging this pull request! |
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Description
Set up process afterscript.
Closes #157
Testing Results
Process log dir - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-process-afterscript/gsv_discovery-all-tools-std-input/call-gSV-5.1.0/HG003/log-call-gSV-5.1.0-20240626T195850Z/process-log/
NFTest log - /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-process-afterscript/sbatch-nftest-20240626T195514Z.log
Checklist
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, am listedalready, 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 with
run_delly = true,run_manta = true,run_qc = true. Forrun_delly = true, I have tested 'variant_type' set togSV,gCNV, and both. The paths to the test config files and output directories are captured above in the Testing Results section.