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Config parser (and loader)

7

Close #2723 This PR explores one possible solution to the config overhaul by implementing a custom parser for config files, using a similar approach as #4613. The linked issue initially...

bentsherman

Failed to sanitize XML document destined for handler class (..) ListBucketHandler

1

### Expected behavior and actual behavior I am running the `fetchngs` [pipeline](https://nf-co.re/fetchngs/1.11.0) using sequera platform - AWS batch - to retrieve a public datasest of about 1000 samples (~10TB data...

adomingues

Task batching

5

Good morning Europe! 😄 This PR implements task grouping as described in #2527. The implementation is inspired by #3905. Each task processor has a "task group collector" that collects tasks...

bentsherman

Job arrays

85

Closes #1477 (and possibly #1427) Summary of changes: - Adds `array` directive to submit tasks as array jobs of a given size - `TaskArrayCollector` collects tasks into arrays and submits...

bentsherman

Migrate to AWS Java SDK v2

4

Nextflow currently uses the AWS Java SDK v1 which is reaching [end of life](https://aws.amazon.com/blogs/developer/announcing-end-of-support-for-aws-sdk-for-java-v1-x-on-december-31-2025/). Additionally, new features are only being added to SDK v2, which will make it difficult to...

bentsherman

Allow to publish timeline, trace and DAG files as a Tower report

5

## New feature Current Tower plugin is only able to use as reports files that are notified with the `onFilePublish` event. This excludes some files generated by Nextflow like the...

jordeu

Add handling of slurm (and other HPC?) task.exitStatus to enhance task.attempt memory and time scaling

2

## New feature I would like to suggest/request that the task.exitStatus from various HPC job failures be handled in such a way that `task.attempt` could be extended to selectively scale...

gdevenyi

Improvement in Spack implementation - shell commands

2

I overlooked this in the first implementation. There are 3 instances of multiple shell commands in the Spack implementation, where I suggest to replace the semicolons with double ampersands; this...

marcodelapierre

docker.fixOwnership not working with busybox's chown

2

## Bug report ### Expected behavior and actual behavior for most containers when docker is enabled, we see the expected behavior: chown is run at the end of a process...

anoronh4

CLI v2

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Closes #3595 To summarize: - `nextflow.cli.*Impl` classes implement the core functionality of each command - `nextflow.cli.v1.*Cmd` classes implement the CLI v1 and pass options to corresponding `*Impl` class - `nextflow.cli.v2.*Cmd`...

bentsherman