Bump external/pipeline-Nextflow-module from b0b2798 to 9db08f0
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@dependabot rebase |
Bumps [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module) from `b0b2798` to `9db08f0`. - [Commits](uclahs-cds/pipeline-Nextflow-module@b0b2798...9db08f0) --- updated-dependencies: - dependency-name: external/pipeline-Nextflow-module dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
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nwiltsie
approved these changes
Mar 5, 2024
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They should be fine though this is a bump in |
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Ah, you're right, I got over-eager. Those won't be covered by these tests. |
nwiltsie
requested changes
Mar 5, 2024
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Huh. So the first time I tried running NFTest it failed... $ tail /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/dependabot/submodules/external/pipeline-Nextflow-module-9db08f0/log-nftest-20240305T183817Z.log
2024-03-05 18:51:11,888 - nextflow - main - DEBUG - > Execution complete -- Goodbye
2024-03-05 18:51:12,019 - nftest.syslog - MainThread - DEBUG - Syslog server at 127.0.0.1:40971 shutting down
2024-03-05 18:51:12,940 - NFTest - MainThread - DEBUG - Test creation time: 2024-03-05 18:38:17.812213+00:00
2024-03-05 18:51:12,941 - NFTest - MainThread - DEBUG - Actual mod time: 2024-03-05 18:50:20.955821+00:00
2024-03-05 18:51:12,941 - NFTest - MainThread - DEBUG - md5 /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/dependabot/submodules/external/pipeline-Nextflow-module-9db08f0/A-mini-n2/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam
2024-03-05 18:51:20,963 - NFTest - MainThread - ERROR - Assertion failed
2024-03-05 18:51:20,964 - NFTest - MainThread - ERROR - Actual: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/dependabot/submodules/external/pipeline-Nextflow-module-9db08f0/A-mini-n2/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam
2024-03-05 18:51:20,964 - NFTest - MainThread - ERROR - Expect: /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam
2024-03-05 18:51:20,964 - NFTest - MainThread - ERROR - ()
2024-03-05 18:51:20,964 - NFTest - MainThread - ERROR - [ failed ]... but then after I did various $ tail /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/dependabot/submodules/external/pipeline-Nextflow-module-9db08f0/log-nftest-20240305T195824Z.log
2024-03-05 20:08:50,510 - NFTest - MainThread - DEBUG - Assertion passed
2024-03-05 20:08:50,511 - NFTest - MainThread - DEBUG - Test creation time: 2024-03-05 19:58:24.524466+00:00
2024-03-05 20:08:50,511 - NFTest - MainThread - DEBUG - Actual mod time: 2024-03-05 20:08:35.134379+00:00
2024-03-05 20:08:50,511 - NFTest - MainThread - DEBUG - md5 /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/dependabot/submodules/external/pipeline-Nextflow-module-9db08f0/A-mini-n2/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.sha512 /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.sha512
2024-03-05 20:08:50,512 - NFTest - MainThread - DEBUG - Assertion passed
2024-03-05 20:08:50,513 - NFTest - MainThread - DEBUG - Test creation time: 2024-03-05 19:58:24.524472+00:00
2024-03-05 20:08:50,513 - NFTest - MainThread - DEBUG - Actual mod time: 2024-03-05 20:08:35.966003+00:00
2024-03-05 20:08:50,513 - NFTest - MainThread - DEBUG - md5 /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/unreleased/dependabot/submodules/external/pipeline-Nextflow-module-9db08f0/A-mini-n2/recalibrate-BAM-1.0.0-rc.4/TWGSAMIN000001/GATK-4.2.4.1/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai.sha512 /hot/software/pipeline/pipeline-recalibrate-BAM/Nextflow/development/output/BWA-MEM2-2.2.1_GATK-4.2.4.1_A-mini_S2-v1.1.5.bam.bai.sha512
2024-03-05 20:08:50,514 - NFTest - MainThread - DEBUG - Assertion passed
2024-03-05 20:08:50,514 - NFTest - MainThread - INFO - [ succeed ]Soooo... I'm somewhat confused, and I can't re-create the original problem I had. Looking back over my terminal output (failed_console.log) it looks like I did all the right things, but something went weird. |
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I don't really see anything that would indicate why it would fail the first time... 🤔 |
yashpatel6
approved these changes
Mar 12, 2024
nwiltsie
approved these changes
Mar 12, 2024
nwiltsie
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Bumps external/pipeline-Nextflow-module from
b0b2798to9db08f0.Commits
9db08f0Add staging to handle special characters in filenames (#36)525aa38Merge pull request #35 from uclahs-cds/sfitz-add-indexFilefcd7ad6Update README.mdde5323bupdate readmebadabb2add indexFileDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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