Piero Dalle Pezze

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...

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 = {...

Fixes #5 . Changes proposed in this pull request: - added thresholds - added thresholds documentation

Module thresholds (WARN / ERROR)

2

we need to define module-specific thresholds triggering potential warnings or errors.

Help documentation

1

Help documentation for BamQC modules