nextflow

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Enable multiple revisions for project repos (first attempt 2024)

43

This PR adds support for handling local copies of multiple revisions of the same pipeline. Key points: * Under `NXF_ASSETS`, each pipeline is now pulled as `/[:]` ; `:` is...

marcodelapierre

## Bug report When running nextflow with AWS Batch, nxf_s3_download() fails to identify an S3 directory as a directory and attempts to download it as a file (i.e. cp dir...

Chris-Cherry

Walk file tree on directory publish

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Close #3372 I just changed the publish dir to explicitly publish each file in a directory. I think it means that if the publish mode is symlink, each file in...

bentsherman

Friendlier job/VM naming for Google Batch

2

## New feature Currently, when Batch is used directly, the job name dictates the naming of the VMs created. For example, the VM name will be the job name appended...

soj-hub

## Bug report The current implementations of human-readable dates and times are ambiguous in terms of their timezone, and in the case of durations, difficult to properly parse. ### Expected...

gdevenyi

Formal grammar and parser

3

This PR adds a custom parser for Nextflow scripts and uses it instead of the Groovy parser. The Nextflow parser is generated from an ANTLR grammar, which currently contains a...

bentsherman

## Bug report  ### Expected behavior and actual behavior I expect the long name to be either trimmed or scrollable. Instead in actuality, it overflows into adjacent cells ###...

gdevenyi

## New feature I would like to request a (static) config option, or perhaps a (dynamic) toggle in the interactive plotly figures to allow me to de-aggregate process resource reports...

gdevenyi

`workDir` implicit variable missing on google batch executor

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## Bug report ### Expected behavior and actual behavior I'm testing running a workflow with the google cloud batch executor. The `$workDir` implicit variable seems to be an empty string...

nebfield

Update: support for target architecture for Spack Wave

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This PR fixes support for target architecture `spackTarget` in the case of Wave Spack builds. Supersedes #4554 to only focus on Spack Arch and ditch Spack version.

marcodelapierre