nextflow

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GCS doesn't support symlinks, so Google Batch executor should use hardlinks

14

## Bug report (Please follow this template replacing the text between parentheses with the requested information) ### Expected behavior and actual behavior When running a pipeline (in this instance nf-core/quantms)...

harper357

Ability to use 'name' attribute with path() output

2

It would be nice if we could change the file output name in the `output` directive, the same way you can do with `input`, like this; ```groovy process FOO {...

stevekm

[proposal] Expose ScriptParser as an extension point

2

The `ScriptParser` class defines how a Nextflow script is executed. It essentially takes a Nextflow script and produces a Groovy class (i.e. `BaseScript`) which, when executed, builds the workflow DAG....

bentsherman

"dry run" option?

15

When using the -resume option, it would be helpful to see which processes are going to be run and which will be reused from the cache. Additionally it would be...

jemunro

Passing an empty value channel to a process causes nextflow to hang

1

If a channel is created via `channel.value()` and passed directly to a process, nextflow hangs forever. ### Expected behavior and actual behavior I assumed that passing `channel.value()` would work for...

human9

Azure Batch: Add disk size to slots calculation

7

## New feature When using Azure Batch, Nextflow will reject a process if it has too many CPUs for the worker machine. ``` Caused by: Process requirement exceeds available CPUs...

adamrtalbot

clusterOptions does not work with CLI flags (LSF executor)

3

## Bug report when specigying a clusterOptions which includes a flag the Grid executor header is constructed wrongly by nextflow e.g profile.config : ``` clusterOptions = { "-g /${_queue_group} -app...

timini

Apply Azure Batch setting to all pools via config

2

## New feature Azure Batch [has a number of settings to apply to a pool](https://www.nextflow.io/docs/latest/azure.html#advanced-settings), such as autoscale, vmType, sku etc. But you must generate this configuration manually for all...

adamrtalbot

nextflow nextflow/23.04.2 and tower.yml

9

## Bug report ### Expected behavior and actual behavior Inlatest version trying tower.yml as described here https://seqera.io/blog/best-practices-for-deploying-pipelines-with-nextflow-tower/ gave a java error ``` ERROR ~ 'com.fasterxml.jackson.core.io.ContentReference com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(java.lang.Object)' -- Check '.nextflow.log' file...

jIskCoder

When importing an operator from a plugin, if you import anything from the same plugin in a different module, it fails with the following error: https://github.com/nextflow-io/nextflow/blob/f1cffd1b28b443aa3fbd9f99404fea84613d85df/modules/nextflow/src/main/groovy/nextflow/plugin/extension/PluginExtensionProvider.groovy#L137-L139 It seems to import...

bentsherman