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List process container images in preview mode #4069

Merged
merged 71 commits into from
Aug 24, 2023
Merged

List process container images in preview mode #4069

merged 71 commits into from
Aug 24, 2023

Commits on Jun 30, 2023

  1. Dump container image for each process during preview run 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman committed Jun 30, 2023
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Commits on Jul 5, 2023

  1. Support any directives, save report to JSON file 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman committed Jul 5, 2023
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Commits on Jul 6, 2023

  1. Add -preview-report CLI option to enable preview report 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman committed Jul 6, 2023
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Commits on Jul 27, 2023

  1. Merge branch 'master' into 3340-preview-container-images

    @bentsherman
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  2. Apply suggestions from review 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman committed Jul 27, 2023
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Commits on Jul 30, 2023

  1. Merge branch 'master' into 3340-preview-container-images

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Commits on Aug 2, 2023

  1. Merge branch '3340-preview-container-images' of github.com:nextflow-i… 

    …o/nextflow into 3340-preview-container-images
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  2. Merge branch 'master' into 3340-preview-container-images

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  3. Rename to PreviewContainersObserver [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  4. Fix minor type error [ci skip] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 2, 2023
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  5. Revert unrelated changes 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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  6. Format JSON as array of objects 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman committed Aug 2, 2023
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  7. Pushing missing log [ci skip] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Commits on Aug 4, 2023

  1. Replace file output with stdout, suppress console output 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman committed Aug 4, 2023
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Commits on Aug 23, 2023

  1. Update Wave and Fusion docs (#4149) 

    
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  2. Fix strict mode docs (#4150) 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  3. Fix bug with K8s resource labels (#4147) [ci fast] 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  4. Add -value option to config command (#4142) 

    
Signed-off-by: Aaron Fishman <uk.afishman@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Aaron Fishman <aaron.fishman@achillestx.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    4 people committed Aug 23, 2023
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  5. Fix Wave disable flag 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  6. Restore Tower CacheManager for backward compatibility 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  7. Increase Wave client max attempts 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  8. Bump nf-amazon@2.1.1 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  9. Bump nf-azure@1.2.0 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  10. Bump nf-tower@1.6.0 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  11. Bump nf-wave@0.11.1 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  12. Update changelog 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  13. [release 23.08.0-edge] Update timestamp and build number [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  14. Enable cloud cache based on environment variable (#4160) 

    
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  15. Minor changes [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  16. Fix typos in source code comments (#4173) [ci fast] 

    Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    mribeirodantas and pditommaso committed Aug 23, 2023
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  17. Add 429 http status code to Wave retriable errors 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  18. Update changelog 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  19. Improve Conda build error report [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  20. Fix Process hangs when using flatten and finish errorStrategy 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  21. Fix Execution should fail if report or timeline file already exists 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  22. Fix env output when changing task workdir 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  23. Improve handling of name-only container env variables 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  24. Document error about trailing backslash with space (#4180) 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  25. Update AWS instructions for creating a custom AMI [ci skip] (#4174) 

    

Signed-off-by: Manuele Simi <manuele.simi@gmail.com>
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    manuelesimi authored and pditommaso committed Aug 23, 2023
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  26. Remove lock file from cloudcache (#4167) 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  27. Fix checkpoint thread termination (#4166) 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    pditommaso committed Aug 23, 2023
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  28. Update tip about modifying maps (#4153) [ci skip] 

    
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  29. Apply K8s Pod metadata to Job (#4057) [ci fast] 

    
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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  30. Remove dockerize launcher classpath file (#4191) [ci fast] 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  31. Fix workflow.container map resolution (#4190) 

    
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  32. Escape semicolons in paths (#4193) 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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    bentsherman authored and pditommaso committed Aug 23, 2023
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  33. Use root user in Wave container based on micromamba (#4038) [ci fast] 

    Signed-off-by: Marco De La Pierre <marco.delapierre@gmail.com>
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    marcodelapierre authored and pditommaso committed Aug 23, 2023
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  34. FIx nested InvocationTargetException (#4192) [ci fast] 

    
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    bentsherman and pditommaso committed Aug 23, 2023
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  35. Fix if-guard on log.trace in trask processor inner class [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  36. Add resource labels support for Azure Batch (#4178) 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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    bentsherman and pditommaso committed Aug 23, 2023
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  37. Bump nf-azure@1.3.0 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  38. Bump nf-cloudcache@0.2.0 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  39. Bump nf-tower@1.6.1 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  40. Bump nf-wave@0.11.2 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  41. Update changelog [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  42. [release 23.08.1-edge] Update timestamp and build number [ci fast]

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  43. Fix security deps in nf-azure plugin 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  44. Add support for Wave native build for singularity 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  45. Bump groovy 3.0.19 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  46. Move containers preview to its own command 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  47. Merge branch 'master' into 3340-preview-container-images

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  48. apply suggestions from review, minor edits 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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  49. Add tests [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  50. Fix & more 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  51. Just a blank [ci skip] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  52. remove extraneous tests 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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  53. update docs [ci fast] 

    Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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Commits on Aug 24, 2023

  1. Add tests [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  2. Add prompt confirmation [ci fast] 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  3. Restructure json result 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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  4. Add Wave dry-run mode + inspect -concretize 

    Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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