nextflow

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Docker builder override option cpu-shares

3

Nextflow Docker builder (DockerBuilder.groovy) generates a .command.run script that appears to hardcode the option `--cpu-shares` of the docker run command. My environment has the following cgroup restriction: `docker run hello-world`...

jtjvanlunenburg

Fix _JAVA_OPTIONS breaking launch exactly like issue #1716

5

Just like in #1716, the _JAVA_OPTIONS variable results in messages like: ``` Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp -Xmx221184m -Xms256m CAPSULE EXCEPTION: Could not parse version line: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch/03166/xcgalaxy/main/staging/59941234/tmp -Xmx221184m...

richard-burhans

4920: Azure Batch supports process.disk directive

2

This PR adds the `process.disk` directive support to Azure Batch. After adding this directive, Azure Batch will: - Factor disk and VM disk size into the number of slots a...

adamrtalbot

The nf-core pipeline template uses a [custom timestamp](https://github.com/nf-core/tools/blob/7785b4cd8d3ce1321832e1a7ae4f2874509e31f4/nf_core/pipeline-template/nextflow.config#L243-L259) in the various report file names: ```groovy def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" }...

bentsherman

Target java17

15

This set Java 17 as target bytecode generation and lang compatibility. TLDR; so far mock created by Spock used cglib, which is not maintained anymore and does not support Java...

pditommaso

## New feature I want to run an optional process only if the user has provided a secret. Example code: ``` workflow SUMMARY_WF { main: OPTIONAL_PROCESS() } process OPTIONAL_PROCESS {...

nick-youngblut

## Bug report ### Expected behavior and actual behavior I have a subworkflow that I'm importing two times and invoking like this: ```nextflow include { ANNOTATE as ANNOTATE_BCR } from...

sralchemab

AWS spot failure - custom error message

2

We recently set the default for `aws.batch.maxSpotAttempts` to `0` in https://github.com/nextflow-io/nextflow/pull/5215 to avoid unexpected costs in cloud. This is good, but it means we go back to the state we...

ewels

Wait until pipeline completes before publishing

2

## New feature Currently, Nextflow will publish files as it proceeds through the pipeline. If it fails, it will halt leaving some files in place. This creates messy output structures...

adamrtalbot

Process cache groups

1

## New feature Sometimes an error in the process is only exposes later on in the pipeline, when a downstream process fails. In these cases, it would be useful to...

adamrtalbot