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# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs)
# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs) <!-- omit in toc -->
[![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)
@ -14,11 +14,11 @@ A repository for hosting Nextflow configuration files containing custom paramete
* [Checking user hostnames](#checking-user-hostnames)
* [Testing](#testing)
* [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs)
* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
* [Pipeline-specific documentation](#pipeline-specific-documentation)
* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
* [Create the pipeline-specific nf-core/configs files](#create-the-pipeline-specific-nf-coreconfigs-files)
* [Help](#help)
## Using an existing config
@ -154,8 +154,12 @@ Note that pipeline-specific configs are not required and should only be added if
Currently documentation is available for the following pipeline within the specific profile:
* ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md)
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
* eager
* [SHH](docs/pipeline/eager/shh.md)
### Enabling pipeline-specific configs within a pipeline

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//Nextflow config file for running on AWS batch
params {
config_profile_description = 'AWSBATCH Cloud Profile'
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'https://aws.amazon.com/batch/'
awsqueue = false
awsregion = 'eu-west-1'
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_description = 'AWSBATCH Cloud Profile'
config_profile_name = 'AWSBATCH'
config_profile_url = 'https://aws.amazon.com/batch/'
awscli = '/home/ec2-user/miniconda/bin/aws'
tracedir = './'
}
process.executor = 'awsbatch'
executor.awscli = '/home/ec2-user/miniconda/bin/aws'
process.queue = params.awsqueue
aws.region = params.awsregion
executor.awscli = params.awscli

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@ -7,6 +7,7 @@ params {
singularity {
enabled = true
envWhitelist = 'TZ'
}
process {

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@ -20,5 +20,5 @@ params {
max_cpus = 32
max_time = 72.h
igenomes_base = '/camp/svc/reference/Genomics/iGenomes'
igenomes_base = '/camp/svc/reference/Genomics/aws-igenomes'
}

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// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_description = 'nf-core/ampliseq BINAC profile provided by nf-core/configs'
}
env {
TZ='Europe/Berlin'
}

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@ -16,9 +16,7 @@ params {
// Specific nf-core/sarek process configuration
process {
withLabel:sentieon {
if (params.sentieon) {
module = 'sentieon/201808.05'
container = null
}
module = {params.sentieon ? 'sentieon/201808.05' : null}
container = {params.sentieon ? null : container}
}
}

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# nf-core/configs: awsbatch Configuration
To be used with `awsbatch`.
Custom queue and region can be entered with `params.awsqueue` and `params.region` respectively.
Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.

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@ -9,13 +9,13 @@ Before running the pipeline you will need to load Nextflow and Singularity using
```bash
## Load Nextflow and Singularity environment modules
module purge
module load Nextflow/0.32.0
module load Nextflow/19.10.0
module load Singularity/2.6.0-foss-2016b
```
A local copy of the iGenomes resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://github.com/nf-core/atacseq/blob/master/docs/configuration/reference_genomes.md) for instructions).
Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://nf-co.re/usage/reference_genomes) for instructions).
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.

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# nf-core/configs: binac ampliseq specific configuration
Extra specific configuration for the ampliseq pipeline.
## Usage
To use, run the pipeline with `-profile binac`.
This will download and launch the ampliseq specific [`binac.config`](../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster.
Example: `nextflow run nf-core/ampliseq -profile binac`
## ampliseq specific configurations for binac
Specific configurations for BINAC has been made for ampliseq.
* Specifies the `TZ` `ENV` variable to be `Europe/Berlin` to fix a QIIME2 issue

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pipeline/ampliseq.config Normal file
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/*
* -------------------------------------------------
* nfcore/ampliseq custom profile Nextflow config file
* -------------------------------------------------
* Config options for custom environments.
* Cluster-specific config options should be saved
* in the conf/pipeline/ampliseq folder and imported
* under a profile name here.
*/
profiles {
binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
}