15 Pull requests merged by 5 people

• Data Lineage workflow outputs fixes

  #6041 merged May 6, 2025

• Use the same antlr4 dep as Groovy 4

  #5990 merged May 6, 2025

• Improve lineage find docs

  #6038 merged May 6, 2025

• Add plugin create command

  #6032 merged May 6, 2025

• Improve output labels

  #6035 merged May 5, 2025

• Data lineage fix find command arguments check

  #6034 merged May 5, 2025

• Support downloading plugins from OCI registries

  #6016 merged May 5, 2025

• Bring topic channels out of preview

  #6030 merged May 5, 2025

• Use channel namespace to access channel factories

  #6029 merged May 5, 2025

• Data lineage programmatic API

  #6003 merged May 2, 2025

• Remove test constructors or mark as TestOnly

  #5216 merged May 2, 2025

• Refactor lineage annotations as list

  #6022 merged May 2, 2025

• Add config error checking to run command

  #5998 merged May 2, 2025

• Document default values for aws.client config settings

  #6023 merged May 1, 2025

• Fix small formatting inconsistencies

  #6024 merged May 1, 2025

9 Pull requests opened by 7 people

• Update plugins documentation

  #6033 opened May 5, 2025

• Add version to the Data Lineage metadata JSON serialization

  #6037 opened May 5, 2025

• Fix config for Trace level logging within the ConfigBuilder class

  #6040 opened May 6, 2025

• Make config parser v2 compatible with AssetManager

  #6042 opened May 6, 2025

• Added a couple of docs admonitions about things that tripped me up

  #6044 opened May 7, 2025

• Data Lineage quick fixes

  #6045 opened May 7, 2025

• 5920 job array with queuesize exceeds queuesize

  #6047 opened May 7, 2025

• Add allowed plugins list

  #6049 opened May 7, 2025

• DOC: Fix selector expression documentation

  #6050 opened May 7, 2025

2 Issues closed by 1 person

• Improve lineage find docs

  #6036 closed May 6, 2025

• Error when using `-with-weblog` option in Nextflow 24.10

  #5443 closed May 2, 2025

10 Issues opened by 8 people

• docs on what can be used for `path(stageName)`

  #6051 opened May 7, 2025

• docs on using closure for `path` param in publishDir

  #6048 opened May 7, 2025

• Make Google Batch mount path configurable

  #6046 opened May 7, 2025

• Lineage: Accept run names

  #6043 opened May 7, 2025

• Not loggin nextflow.config.ConfigBuilder trace when required

  #6039 opened May 6, 2025

• Using AWS Batch with a pre-defined Job Definition

  #6031 opened May 3, 2025

• Make script loader v2 compatible with console

  #6028 opened May 2, 2025

• Make config parser v2 compatible with AssetManager

  #6027 opened May 2, 2025

• Combining with empty list should produce a list

  #6026 opened May 2, 2025

• Add support for uploading results to AWS S3 with SHA256 ETags using publishDir

  #6025 opened May 1, 2025

83 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Workflow params definition (first preview)

  #5929 commented on May 5, 2025 • 9 new comments

• Remove URL fragment in lineage IDs

  #6011 commented on May 6, 2025 • 4 new comments

• Fix task progress percentage with failed tasks

  #5868 commented on May 6, 2025 • 3 new comments

• Add timezone to date format

  #6013 commented on May 5, 2025 • 0 new comments

• Make Bash path configurable

  #5696 commented on May 5, 2025 • 0 new comments

• Azure Batch worker pool supports managed identity

  #5670 commented on May 5, 2025 • 0 new comments

• Identity-based provenance tracking

  #5639 commented on May 5, 2025 • 0 new comments

• Add whitespace rules to `.editorconfig`

  #5606 commented on May 5, 2025 • 0 new comments

• Update bin, lib, template docs

  #5564 commented on May 5, 2025 • 0 new comments

• Headless release

  #5554 commented on May 5, 2025 • 0 new comments

• Support not using a container in Azure Batch

  #5536 commented on May 5, 2025 • 0 new comments

• Fix PBSPRO queue status fetch

  #5529 commented on May 5, 2025 • 0 new comments

• Fix hash when CmdEvalParam as output

  #5517 commented on May 5, 2025 • 0 new comments

• Include job status report when failure and no exit code found

  #5514 commented on May 5, 2025 • 0 new comments

• Warn when `file()` matches a collection of files

  #5507 commented on May 5, 2025 • 0 new comments

• Use `conda-forge` and `bioconda` channels by default

  #5423 commented on May 5, 2025 • 0 new comments

• Enable AWS secrets manager

  #5395 commented on May 5, 2025 • 0 new comments

• Fix workflow onComplete and onError in the entry workflow

  #5366 commented on May 5, 2025 • 0 new comments

• Hash improvements

  #5351 commented on May 5, 2025 • 0 new comments

• Recommend using Nextflow secrets for sensitive credentials in configs

  #5227 commented on May 5, 2025 • 0 new comments

• Use explicit memory units for LSF executor

  #5217 commented on May 5, 2025 • 0 new comments

• Fix unescaped spaces and parentheses in container env script

  #5193 commented on May 5, 2025 • 0 new comments

• Upgrade kryo to 5.4.0

  #3562 commented on May 5, 2025 • 0 new comments

• Remove obsolete conda create --mkdir option

  #6010 commented on May 6, 2025 • 0 new comments

• Fix: Allow running pipelines from local file:/ Git repositories in offline mode

  #6007 commented on May 6, 2025 • 0 new comments

• Fix stack overflow error with workflow metadata

  #5988 commented on May 5, 2025 • 0 new comments

• Solve issue with losing track of SLURM jobs using cephfs

  #5976 commented on May 5, 2025 • 0 new comments

• Separate CLI from runtime

  #5971 commented on May 5, 2025 • 0 new comments

• Add support for container build compression

  #5964 commented on May 5, 2025 • 0 new comments

• Print process dictionary in logs (#5940)

  #5944 commented on May 5, 2025 • 0 new comments

• Add a documentation note about AWS_PROFILE

  #5931 commented on May 5, 2025 • 0 new comments

• New executor for Fujitsu Technical Computing Suite (TCS)

  #5928 commented on May 5, 2025 • 0 new comments

• Update git tests

  #5927 commented on May 5, 2025 • 0 new comments

• Include remote path in FileHolder

  #5911 commented on May 5, 2025 • 0 new comments

• Extend observer with onFileStage

  #5907 commented on May 5, 2025 • 0 new comments

• Add Conda install to install page

  #5892 commented on May 5, 2025 • 0 new comments

• Support prefetching plugins metadata from an http api

  #5887 commented on May 5, 2025 • 0 new comments

• Add Fusion support to HTCondor

  #5865 commented on May 5, 2025 • 0 new comments

• Move troubleshooting to new docs section

  #5856 commented on May 5, 2025 • 0 new comments

• Manage NVIDIA GPU slots in local executor

  #5850 commented on May 5, 2025 • 0 new comments

• feat(AzBatchTaskHandler): Include other output files in final upload statement

  #5803 commented on May 5, 2025 • 0 new comments

• Treat LSF job status UNKWN as HOLD

  #5756 commented on May 5, 2025 • 0 new comments

• Micronaut DI support

  #3499 commented on May 5, 2025 • 0 new comments

• add support for mpijobs via kubeflow operator

  #3392 commented on May 5, 2025 • 0 new comments

• Fix `process.ext` set with `withName` overrides all processes

  #2783 commented on May 5, 2025 • 0 new comments

• [New Feature] Evaluate Closure for every input file

  #2622 commented on May 5, 2025 • 0 new comments

• Test cases for configuration parsing

  #2498 commented on May 5, 2025 • 0 new comments

• [New Feature] Group tuple size

  #2489 commented on May 5, 2025 • 0 new comments

• [Bugfix] Fix broken symlinks with scratch and move

  #2478 commented on May 5, 2025 • 0 new comments

• Tests for unstage strategy and fix for special characters

  #2181 commented on May 5, 2025 • 0 new comments

• Azure can use preempted nodes within nodes

  #5545 commented on May 6, 2025 • 0 new comments

• Conda: Support `.lock` file extensions.

  #5583 commented on May 6, 2025 • 0 new comments

• `groupTuple` results can be invalid if key contains `ArrayBag`

  #4466 commented on May 6, 2025 • 0 new comments

• New method templateFile for replacing template variables in a file resource with values from context

  #5962 commented on May 5, 2025 • 0 new comments

• Use `-resume` with run names in addition to session IDs

  #4837 commented on May 5, 2025 • 0 new comments

• Provide a special class for pipeline-defined error messages

  #4937 commented on May 5, 2025 • 0 new comments

• Allow custom configs `params` to be parsed before nextflow.config

  #2662 commented on May 5, 2025 • 0 new comments

• Add gzip (de)compression support to the collectFile operator

  #3071 commented on May 5, 2025 • 0 new comments

• Job arrays support for HTCondor

  #5960 commented on May 2, 2025 • 0 new comments

• Usage of secrets in Workflow Script on AWS Batch and Platform

  #5943 commented on May 2, 2025 • 0 new comments

• Workflow onComplete/onError handlers don't work when defined in the entry workflow

  #5261 commented on May 1, 2025 • 0 new comments

• Allow the concurrent run of multiple pipeline revisions

  #2870 commented on May 1, 2025 • 0 new comments

• Enable multiple git revisions (Jun 2024) : final, using commit ID in repo localPath

  #5089 commented on May 5, 2025 • 0 new comments

• Enable multiple git revisions (Jan-Apr 2024) : temporary, using revision name in repo localPath

  #5087 commented on May 5, 2025 • 0 new comments

• Allow dynamic `cache` directives using closures

  #5044 commented on May 5, 2025 • 0 new comments

• Add labels to Wave container config

  #4817 commented on May 5, 2025 • 0 new comments

• feat: remove storage account name if present from azure path

  #4692 commented on May 5, 2025 • 0 new comments

• Enable multiple revisions for project repos (first attempt 2024)

  #4659 commented on May 5, 2025 • 0 new comments

• Improve logging of task progress

  #4588 commented on May 5, 2025 • 0 new comments

• Static types for process inputs/outputs

  #4553 commented on May 5, 2025 • 0 new comments

• Support specifying disk image for additional disk with Google Batch

  #4535 commented on May 5, 2025 • 0 new comments

• Add `checksum` option to `file()` for verifying http/ftp files

  #4415 commented on May 5, 2025 • 0 new comments

• Include FileHolder stage name in task cache

  #4301 commented on May 5, 2025 • 0 new comments

• Fix issues with workflow complete handler

  #4299 commented on May 5, 2025 • 0 new comments

• More helpful warnings when publish fails to create parent directory

  #4241 commented on May 5, 2025 • 0 new comments

• Dry run

  #4214 commented on May 5, 2025 • 0 new comments

• Remove privileged mode with Fusion

  #4141 commented on May 5, 2025 • 0 new comments

• Prefer to use CacheFunnel implementation when available for caching non-trivial objects

  #4077 commented on May 5, 2025 • 0 new comments

• Walk file tree on directory publish

  #3933 commented on May 5, 2025 • 0 new comments

• Add snake_case to params normalization

  #3884 commented on May 5, 2025 • 0 new comments

• Automatic task cleanup

  #3849 commented on May 5, 2025 • 0 new comments

• CLI v2

  #3600 commented on May 5, 2025 • 0 new comments

• Add support for checksum algorithm for S3 uploads

  #3585 commented on May 5, 2025 • 0 new comments