From 08a6b748250c26147fc61b827598fef6a5e0a22a Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 10 Oct 2019 15:33:06 +0200 Subject: [PATCH 1/2] add new profile to be shared: awsbatch --- README.md | 9 +++++---- conf/awsbatch.config | 14 ++++++++++++++ docs/awsbatch.md | 4 ++++ nfcore_custom.config | 1 + 4 files changed, 24 insertions(+), 4 deletions(-) create mode 100644 conf/awsbatch.config create mode 100644 docs/awsbatch.md diff --git a/README.md b/README.md index d9cc35f..3ef16e0 100644 --- a/README.md +++ b/README.md @@ -16,15 +16,15 @@ A repository for hosting nextflow config files containing custom parameters requ ## Using an existing config -The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation. +The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organization are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organization. ### Configuration and parameters The config files hosted in this repository define a set of parameters which are specific to compute environments at different Institutions but generic enough to be used with all nf-core pipelines. -All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customise the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines. +All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customize the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines. -You should be able to get a good idea as to how other people are customising the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf). +You should be able to get a good idea as to how other people are customizing the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf). ### Offline usage @@ -80,8 +80,9 @@ You will have to create a [Markdown document](https://www.markdownguide.org/gett See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples. -Currently documentation is available for the following clusters: +Currently documentation is available for the following systems: +* [AWSBATCH](docs/awsbatch.md) * [BIGPURPLE](docs/bigpurple.md) * [BINAC](docs/binac.md) * [CBE](docs/cbe.md) diff --git a/conf/awsbatch.config b/conf/awsbatch.config new file mode 100644 index 0000000..978da56 --- /dev/null +++ b/conf/awsbatch.config @@ -0,0 +1,14 @@ +//Nextflow config file for running on AWS batch + +params { + config_profile_name = 'AWSBATCH' + config_profile_description = 'AWSBATCH Cloud Profile' + config_profile_contact = 'Alexander Peltzer (@apeltzer)' + config_profile_url = 'https://aws.amazon.com/batch/' +} + +aws.region = params.awsregion +process.executor = 'awsbatch' +process.queue = params.awsqueue +executor.awscli = '/home/ec2-user/miniconda/bin/aws' +params.tracedir = './' \ No newline at end of file diff --git a/docs/awsbatch.md b/docs/awsbatch.md new file mode 100644 index 0000000..bec4d78 --- /dev/null +++ b/docs/awsbatch.md @@ -0,0 +1,4 @@ +# nf-core/configs: awsbatch Configuration + +To be used with `awsbatch`. +Custom queue and region can be entered with `params.awsqueue` and `params.region` respectively. \ No newline at end of file diff --git a/nfcore_custom.config b/nfcore_custom.config index 9ec9ade..cceb01c 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -12,6 +12,7 @@ params.custom_config_version = 'master' params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" profiles { + awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" } bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" } binac { includeConfig "${params.custom_config_base}/conf/binac.config" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } From cb1c2eacd05476a6a359e1602a95b9bbc91bf92f Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 19 Nov 2019 16:36:51 +0100 Subject: [PATCH 2/2] Z->S --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3ef16e0..b9812b6 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ A repository for hosting nextflow config files containing custom parameters requ ## Using an existing config -The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organization are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organization. +The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation. ### Configuration and parameters @@ -24,7 +24,7 @@ The config files hosted in this repository define a set of parameters which are All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customize the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines. -You should be able to get a good idea as to how other people are customizing the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf). +You should be able to get a good idea as to how other people are customising the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf). ### Offline usage