nextflow

nextflow copied to clipboard

New feature: bridge executor

2

## New feature Hi nextflow community. I'd like to propose a new feature for nextflow: a new executor based on the "bridge" scheduler. Bridge is an abstraction layer to ease...

erbon7

Add an intdiv method to nextflow.util.MemoryUnit

2

## New feature Is it possible to implement an `intdiv()` method in `nextflow.util.MemoryUnit` as followed?. ```groovy assert 7.GB == (15.GB).intdiv(2) ``` ## Usage scenario I would like to assign a...

jinmingda

AWS batch "too many requests" errors are not retriable

3

Hello. Regarding this line and the similar logic in the functions around it: https://github.com/nextflow-io/nextflow/blob/b099d430aa06b350ff63b6f3ae291dd72f49c779/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy#L767 We have seen quite a few TooManyRequests exceptions when Batch is under high load. They should...

jwarwick-delfi

Add notes about merge, multiMap, and multiple input channels

1

From some other discussions (#2113 #2682), it looks like some users like to use the following pattern: 1. start with a channel of tuples or maps 2. use `multiMap` to...

bentsherman

Error while publishing directories on azure

10

## Bug report ### Expected behavior and actual behavior On the microsoft azure platform, when a process outputs a directory containing files and subfolders, nextflow fails to copy these to...

fbdtemme

Error trying to pull Azure Open Data sets

14

## Bug report ### Expected behavior and actual behavior Expected to be able to provide path to Azure open data sets and download using the https path. However it tries...

vsmalladi

Missing plugin 'nf-amazon' required to read file

14

Hello, I run my nextflow pipeline within a docker container in a kubernetes environment. I have troubles with the plugin `nf-amazon` . In particular: 1. `nextflow plugins install nf-amazon` does...

pdp10

storeDir don't reproduce the correct output tuple in the output channel

2

## Bug report When storeDir is used with an output tuple, the channel doesn't produce the expected output. ### Expected behavior and actual behavior Output without storeDir: [1, /home/X/work/e6/23dc34e4d6f87b5a6f6a3faa340a97/1.txt] [2,...

courcelm

Configure errorStrategy and memory in a process using env vars.

3

Hi, I am trying to get this work: ``` withName:my_process { container = "${env.MY_DOCKER_IMAGE}" cpus = "${env.K8S_CPU}" memory = { "${env.K8S_MEM_HIGH}" * task.attempt } maxRetries = 3 errorStrategy = {...

pdp10

Add a `clean` parameter to `publishDir`

3

## New feature A `clean` parameter added to `publishDir`. Example: ``` publishDir path: 's3://path/to/output`, clean: true ``` ## Usage scenario Often times the output filenames change during development of a...

massung