Update versions for five tools #323
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sorelfitzgibbon
requested review from
tyamaguchi-ucla,
yashpatel6,
maotian06 and
a team
as code owners
|
Bleep bloop, I am a robot. Alas, some of the Nextflow configuration tests failed! test/configtest-F16.json@ ["params","BCFtools_version"]
- "1.17"
+ "1.21"
@ ["params","GATK_version"]
- "4.5.0.0"
+ "4.6.1.0"
@ ["params","MuSE_version"]
- "2.0.4"
+ "2.1.2"
@ ["params","bam_readcount_version"]
- "0.8.0"
+ "1.0.1"
@ ["params","docker_image_BCFtools"]
- "ghcr.io/uclahs-cds/bcftools:1.17"
+ "ghcr.io/uclahs-cds/bcftools:1.21"
@ ["params","docker_image_GATK"]
- "broadinstitute/gatk:4.5.0.0"
+ "broadinstitute/gatk:4.6.1.0"
@ ["params","docker_image_MuSE"]
- "ghcr.io/uclahs-cds/muse:2.0.4"
+ "ghcr.io/uclahs-cds/muse:2.1.2"
@ ["params","docker_image_bam_readcount"]
- "ghcr.io/uclahs-cds/bam-readcount:0.8.0"
+ "ghcr.io/uclahs-cds/bam_readcount:1.0.1"
@ ["params","docker_image_validate_params"]
- "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2"
+ "ghcr.io/uclahs-cds/pipeval:5.1.0"
@ ["params","pipeval_version"]
- "4.0.0-rc.2"
+ "5.1.0"test/configtest-F32.json@ ["params","BCFtools_version"]
- "1.17"
+ "1.21"
@ ["params","GATK_version"]
- "4.5.0.0"
+ "4.6.1.0"
@ ["params","MuSE_version"]
- "2.0.4"
+ "2.1.2"
@ ["params","bam_readcount_version"]
- "0.8.0"
+ "1.0.1"
@ ["params","docker_image_BCFtools"]
- "ghcr.io/uclahs-cds/bcftools:1.17"
+ "ghcr.io/uclahs-cds/bcftools:1.21"
@ ["params","docker_image_GATK"]
- "broadinstitute/gatk:4.5.0.0"
+ "broadinstitute/gatk:4.6.1.0"
@ ["params","docker_image_MuSE"]
- "ghcr.io/uclahs-cds/muse:2.0.4"
+ "ghcr.io/uclahs-cds/muse:2.1.2"
@ ["params","docker_image_bam_readcount"]
- "ghcr.io/uclahs-cds/bam-readcount:0.8.0"
+ "ghcr.io/uclahs-cds/bam_readcount:1.0.1"
@ ["params","docker_image_validate_params"]
- "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2"
+ "ghcr.io/uclahs-cds/pipeval:5.1.0"
@ ["params","pipeval_version"]
- "4.0.0-rc.2"
+ "5.1.0"If the above changes are surprising, stop and determine what happened. If the above changes are expected, there are two ways to fix this:
|
|
/fix-tests |
|
Bleep bloop, I am a robot. I have updated all of the failing tests for you with e6cbd00. You must review my work before merging this pull request! |
Wiz Scan Summary
To detect these findings earlier in the dev lifecycle, try using Wiz Code VS Code Extension. |
yashpatel6
approved these changes
Nov 4, 2024
CHANGELOG.md
Outdated
| @@ -5,6 +5,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | |||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | |||
|
|
|||
| ## [Unreleased] | |||
| ### Changed | |||
| - Update pipeval 4.0.0-rc.2 -> 5.1.0 | |||
There was a problem hiding this comment.
chore
Suggested change
| - Update pipeval 4.0.0-rc.2 -> 5.1.0 | |
| - Update PipeVal 4.0.0-rc.2 -> 5.1.0 |
…all-sSNV into sfitz-update-tools
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Description
Updates:
pipeval_version = "5.1.0"
GATK_version = "4.6.1.0"
bam_readcount_version = "1.0.1"
MuSE_version = "2.1.2"
BCFtools_version = "1.21"
PR template
NFtest files were updated due to new GATK output format:
I confirmed no additional changes beyond these.
Closes #316, #315, #311
Testing Results
nftest
a_mini-all-tools-std-input
log:
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-update-tools/log-nftest-20241103T043500Z.loga_mini-all-tools-vcf-input
log:
/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-update-tools/log-nftest-20241103T154435Z.logChecklist
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.