nextflow

nextflow copied to clipboard

Improve packaging and distribution system

3

## Summary Nextflow application is a packaged as a set of JAR files (Java archives) that are uploaded to [Maven central repository](https://search.maven.org/) with the exception of the launcher app that's...

pditommaso

"cleanup" option does not remove staged files from S3

3

## Bug report When using Nextflow with the `cleanup = true` option, input files staged from S3 are left in the work dir. ### Expected behavior and actual behavior In...

stevekm

Endpoint url error

5

## Bug report Nextflow file main.nf ``` #!/usr/bin/env nextflow params.values = Channel.from(1) process echoValue { publishDir "${params.outdir}/echoValue/", mode: 'copy' input: val value output: path "*_echoValue.txt" script: """ echo "Value: $value"...

nttg8100

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

4

This PR is spawned out of #4659, of which it represents its evolution and finalisation. Some highlights: * handles multiple revisions by storing them in `localPath` defined via the `commitId`,...

marcodelapierre

## Bug report On google-batch, when using a different service account than the default one, it seems both the default service account (scheduling the jobs) and the runner service account...

Puumanamana

New introspection `workflow.seqeraPlatform` scope for data from Seqera Platform

4

It'd be nice to have a new workflow introspection scope called `workflow.seqeraPlatform` to access metadata from Seqera Platform, when available. For example: ```nextflow workflow.seqeraPlatform.user.username workflow.seqeraPlatform.user.name workflow.seqeraPlatform.user.email workflow.seqeraPlatform.user.roles workflow.seqeraPlatform.workspace.id workflow.seqeraPlatform.workspace.name workflow.seqeraPlatform.computeEnvironment.id...

ewels

Hello, I'm trying out the new publish feature introduced in version 24.04.0, but wasn't able to figure out the right implementation in my case. In my current pipeline, a single...

Puumanamana

Mixing of function scope to two separate calls to same Groovy function from separate workflows

2

## Bug report This is a very peculiar bug involving an apparent breakdown of scope when the same Groovy method is called by two subworkflows in parallel. The smallest example...

bskubi

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

1

This is spawned out of #4659 . Original attempt, using revisions not commit IDs, in localPath (as per original thread). This PR is for the record and for reference, unlikely...

marcodelapierre

"Missing project main script" error when there is a directory with the workflow name

3

## Bug report ### Expected behavior and actual behavior **Expected behaviour** Pipelines runs successfully **Actual behaviour** **Nextflow** exist with a `Missing project main script` error when run in a specific...

lazappi