nextflow

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Build java22

2

This PR adds the support Java 22

pditommaso

Provide a special class for pipeline-defined error messages

4

## New feature It would be nice to have a special error class or function for pipeline-level errors or warnings, that help distinguish pipeline-defined (conditional) errors versus Nextflow level errors...

jfy133

Allow multiple cluster options to be specified as a string list

1

Close #4935 - Allow `clusterOptions` to be a string or string list - Each list element is written to a separate line when required by the executor, otherwise the list...

bentsherman

Order of 'includeConfig' and 'profiles' in nextflow.config seems to affect nested property overrides

5

## Bug report ### Expected behavior and actual behavior Hi Nextflow team, I expected that the order in which 'includeConfig' and 'profiles' are declared in nextflow.config would have no effect...

danoreper

storeDir is not working

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## Bug report Using storeDir makes the pipeline crash complaining that the required output file is not there any more. ### Expected behavior and actual behavior In past storeDir was...

lucacozzuto

User Defined Managed Identity Authentication for Azure VM/Batch

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## New feature Allow Azure Batch VMs to be authenticated with User Assigned Managed Identity when the pool is correctly configured. This will prevent to leak secrets into nextflow configuration...

swampie

`filterMap` operator

3

## New feature: `filterMap` operator Nextflow currently supports both the `filter` and `map` operators against a queue channel. It is very common to combine these, so it may be useful...

Xophmeister

Pin only major/minor plugin version with `+` suffix

19

Close #4329 This PR changes the plugin system to not download plugins in offline mode (`NXF_OFFLINE`). Instead, Nextflow will search the plugins directory for the latest plugin version and use...

bentsherman

Institution/Cluster level config

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## New feature We would like to implement some required config for our whole cluster. This would include required tracer plugins and default executors etc. nf-core provides this through the...

chris-cheshire

Fix bug with tap op and value channel

2

This PR fixes a bug with the tap operator which causes it to hang forever when given a value channel. I also removed the IntoOp class as it is essentially...

bentsherman