nextflow

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[New Feature] Group tuple size

2

Today I spent some time finding out how to group tuples when the group sizes vary. Currently, I have to do it this way. ``` Channel .from( [1,'A'], [1,'B'], [2,'C'],...

Lehmann-Fabian

Modify slurm executor to support cluster [closes #2473]

4

Hi @pditommaso , I had a stab at adding the cluster directive. This is my first contact with your project and with Groovy so I hope I did not make...

knservis

[Bugfix] Fix broken symlinks with scratch and move

11

In an old version of [nf-core/viralrecon](https://github.com/nf-core/viralrecon/) I found the following code: https://github.com/nf-core/viralrecon/blob/75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a/main.nf#L660-L661 Creating symlinks leads to problems if the workflow is executed in a scratch directory, moving the outputs. This...

Lehmann-Fabian

## Description Current implementation only allows to use `baseDir`, `projectDir`, `launchDir` and `secrets` at the parameters file or from the command line. This pull request adds also the option to...

jordeu

PublishDir allows closures for mode, enabled, overwrite fields

8

This is a suggestion to make `PublishDir` more flexible by allowing more of the fields to be set using a closure. ### Use Case I am using logic suggested here...

mjhipp

Add docs for process.cleanup

8

Following up from the discussion earlier today.

abhi18av

Add missing config for Azure repos integration

2

I noticed that even though[ tests](https://github.com/nextflow-io/nextflow/blob/78570b11e77e26cb9d607b28e929816bcbbc28ff/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy#L29) seem to indicate there are more config fields they seemed to be missing from the docs.

abhi18av

This PR solves the problem of missing escape for output file names containing glob characters

pditommaso

I found a hidden option - https://github.com/nextflow-io/nextflow/blob/1e485b32b25ba5a369696c2080432eb06391d641/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy#L119 This option is actually valuable. Basically, the bin dir is not namespaced - processes download it to `/tmp/nextflow-bin`. Now, if you mount in...

jchorl

As I promised in my PR [https://github.com/nextflow-io/nextflow/pull/2035](https://github.com/nextflow-io/nextflow/pull/2035), I copied my tests into a new branch and adjusted them to the new logic. I also fixed problems with special characters. So...

Lehmann-Fabian