diff --git a/markdown/usage/installation.md b/markdown/usage/installation.md index 6f769d25c8..aefd23dc6f 100644 --- a/markdown/usage/installation.md +++ b/markdown/usage/installation.md @@ -3,7 +3,7 @@ title: Installation subtitle: Installing the building blocks needed for running nf-core pipelines. --- -This documentation assumes that you have already read the [introduction](introduction.md) and are familiar with the tools described below. +This documentation assumes that you have already read the [introduction](usage/introduction) and are familiar with the tools described below. # Table of contents @@ -67,7 +67,41 @@ If you would like to make changes to the pipeline, it's best to make a fork on G ## Pipeline configuration -By default, the pipeline loads a basic server configuration [`conf/base.config`](../conf/base.config) +By default, the pipeline loads a basic resource configuration: +```bash +process { + + cpus = { check_max( 2, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 2.h * task.attempt, 'time' ) } + + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'terminate' } + maxRetries = 1 + maxErrors = '-1' + + // Process-specific resource requirements + withName: fastqc { + time = { check_max( 8.h * task.attempt, 'time' ) } + } + withName:toolX { + cpus = { check_max( 8, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + } + withName: toolY { + cpus = { check_max( 10, 'cpus' ) } + memory = { check_max( 200.GB * task.attempt, 'memory' ) } + time = { check_max( 5.h * task.attempt, 'time' ) } + } +} + +params { + // Defaults only, expecting to be overwritten + max_memory = 128.GB + max_cpus = 16 + max_time = 240.h + igenomes_base = 's3://ngi-igenomes/igenomes/' +} +``` This uses a number of sensible defaults for process requirements and is suitable for running on a simple (if powerful!) local server. diff --git a/public_html/usage/introduction.php b/public_html/usage/introduction.php index 6bbf41681f..fff0279ee2 100644 --- a/public_html/usage/introduction.php +++ b/public_html/usage/introduction.php @@ -1,6 +1,6 @@