nextflow

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two input variables with identical names are allowed

3

## Bug report Nextflow seems to allow multiple input variables with identical names in the same process, which could lead to unexpected behavior. ### Expected behavior and actual behavior Nextflow...

jgbaum

Recursively downloading S3 directory restored from Glacier doesn't work

13

## New feature For rnasplice pipeline, I wanted to provide my previous salmon output as an input as suggested [here](https://nf-co.re/rnasplice/1.0.2/docs/usage#salmon-quantification-files) So I prepared input sheet like this: sample,condition,salmon_results xyz,case,s3://bucket/path/salmon/xyz where...

Mridul-Chaudhary

splitFastq does not split beyond the second file in PE mode

2

## Bug report (Please follow this template replacing the text between parentheses with the requested information) ### Expected behavior and actual behavior The current Nextflow docs for `splitFastq` states: >Finally...

JohnMMa

Fix console "Plugin manager not initialised" warn

1

This PR fixed the warning reported by the Console when running a script more then one time > WARN: Plugin manager not initialised -- Using built-in executors

pditommaso

Add 'preview' to workflow runtime metadata

1

This addresses #4478. I more-or-less copied the implementation of the `stubRun` property.

greenberga

Sub-workflow is not inheriting replaced param values

5

## Bug report ### Expected behavior and actual behavior When calling `.replace` on the `params` object in `main.nf`, I would expect that any access to the `params` object in any...

nh13

Configuration file variable interpolation does not respect source order

1

## Bug report ### Expected behavior and actual behavior Expected behaviour: When using [variable interpolation in the nextflow.config file](https://www.nextflow.io/docs/stable/config.html#config-variables), I expect parameters provided on the command line to override the...

mluypaert

join doesn't match the same keys

4

## Bug report ### Expected behavior and actual behavior Sometimes join function fails matching entries with same key values. Tricky bit is that this happens most of the time but...

berguner

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

5

## New feature It should be possible to also use run ID `-names` with the `-resume` flag when a user wants to refer to a specific previous pipeline run to...

jfy133

Nextflow does not work with the latest version of Java (22): ``` ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later...

bounlu