nextflow

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Code executed using 'exec' is executed outside of work directory

4

## Bug report ### Expected behavior and actual behavior The [documentation](https://www.nextflow.io/docs/latest/process.html#native-execution) says that I can just replace a script command with Groovy language code to do some processing. However, when...

ssadedin

Evolution of Nextflow configuration file

28

### Rationale The configuration file is a key component of the Nextflow framework since it allows workflow developers to decouple the pipeline logic from the execution parameters and infrastructure deployment...

pditommaso

Implicit variables are null when using kuberun

21

## Bug report ### Expected behavior and actual behavior When I use `${baseDir}` in my config file, it is properly recognized when I run my pipeline using `nextflow run`: ```...

bentsherman

process.executor is not recognized for certain nextflow versions and process orders in the configs

9

## Bug report ### Expected behavior and actual behavior **TLDR: `process.executor = 'google-lifesciences'` is not recognized for certain nextflow versions if its written before another process {} statment**. We have...

replikation

process.ext set with withName overrides configuration of all processes

7

## Bug report ### Expected behavior and actual behavior * Expected: Options set with `withName` only affect the corresponding process(es) * Actual: If process.ext gets initalized for all processes, updating...

grst

Add new executor to nextflow: Bridge (see issue #3094).

erbon7

PBS Torque - Node architecture

7

## New feature Hello there :wave:, I'm facing some problems when using nextflow on a PBS/torque node with hybrid architecture (2 nodes on ppc7 + 1 x86 node), and this...

Mxrcon

Enhance the azcopy options configuration scope

4

This PR builds upon the available settings with the core `azcopy` tool which is used for uploads and downloads in the context of Azure Blob storage service.

abhi18av

Job array for more efficient SGE cluster management

17

I am using nextflow with a SGE task scheduler. I've noticed that the pipeline submits many very similar jobs that are batched across a number of samples (e.g., FastQC on...

mgandal

Path includeInputs does not work for symlinks

10

Try ``` process foo { input: path x from '/some/data/foo.txt' output: path '*', includeInputs:true into foo_ch """ touch file.txt """ } foo_ch.view { "foo: $it.name" } ````

pditommaso