Update nextflow version to 22.10.7 #196
Comments
jaserud
changed the title
lindaxiang
changed the title
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We need to upgrade |
Co-authored-by: UmmulkiramR <[email protected]>
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works with the new version on QA now. |
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The workflows triggered with the new version execute successfully the first time. For the subsequent runs, however, the library keeps throwing the After reaching out to the nextflow developers they requested for a github issue to be raised for this. |
Buwujiu
added
blocker
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The Nextflow team converted the 4018 bug report to a discussion. Here's the link -> nextflow-io/nextflow#4019 |
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can we make our own nextflow version and use it until they release a new version? |
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Management in dev and QA now uses the forked version of the nextflow library that contains the bug fix. Works for both prealnqc and dnaalnqc workflows as tested by @lindaxiang here -> icgc-argo/workflow-roadmap#388 |
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PR created on the original nextflow repo -> nextflow-io/nextflow#4355 |
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In the meantime, have forked the Nextflow library into our icgc-argo repo and added the proposed fix in there to unblock workflows in RDPC. We need to plan a release of WF management to prod that uses this forked version of the Nextflow library |
* upgrade springboot 2.6.6 and misc dependencies (#200) * cannot start runs on prod #204 -- added config params to enable rabbitmq consumers to reconnect when the connection breaks. * Develop with loggers (#208) * Added logger statements * Added logger statements * research and investigation Co-authored-by: UmmulkiramR <[email protected]> * removed some logging (#211) Co-authored-by: UmmulkiramR <[email protected]> * updated nextflow version for #196 (#212) Co-authored-by: UmmulkiramR <[email protected]> * Nextflow 22 10 7 plugin fix (#213) * changed nextflow library version to use the forked copy that contains the plugins fix * changed repository name * add github token for maven packages --------- Co-authored-by: UmmulkiramR <[email protected]> Co-authored-by: Anders Richardsson <[email protected]> * readme update (#216) * updated readme with instructions on how to use the forked version of the nextflow library * Update README.md Co-authored-by: Anders Richardsson <[email protected]> * Update README.md Co-authored-by: Anders Richardsson <[email protected]> * Update README.md Co-authored-by: Anders Richardsson <[email protected]> * Update README.md Co-authored-by: Anders Richardsson <[email protected]> * Update README.md Co-authored-by: Anders Richardsson <[email protected]> * Update README.md Co-authored-by: Anders Richardsson <[email protected]> * added review suggestions. --------- Co-authored-by: UmmulkiramR <[email protected]> Co-authored-by: Anders Richardsson <[email protected]> * Jenkins migration (#217) * Update Jenkinsfile * docker file update for adding server.xml for maven --------- Co-authored-by: Yelizar Alturmessov <[email protected]> Co-authored-by: UmmulkiramR <[email protected]> * test command edit (#218) Co-authored-by: UmmulkiramR <[email protected]> * update to 3.6.0 contains: - nextflow version change with the forked library - Jenkins file update for cumulus build pipelines. --------- Co-authored-by: jaserud <[email protected]> Co-authored-by: UmmulkiramR <[email protected]> Co-authored-by: Anders Richardsson <[email protected]> Co-authored-by: Anders Richardsson <[email protected]> Co-authored-by: Yelizar Alturmessov <[email protected]>
Detailed Description
21.04.3Possible Implementation
Current Challenge
Nextflow new version has a bug, if we upgrade, our system will break. The older version affects running any WF.
Edmund is not blocked, he's on germline VC pipeline. Needs to run benchmarking test before needing the version upgrade.
Bug raised in nextflow: nextflow-io/nextflow#4019
Updates
Give them our PR, and see if they respond?
Check if they have any contribution guide.
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