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README.md
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README.md
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# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs)
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# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs) <!-- omit in toc -->
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[![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)
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@ -14,11 +14,11 @@ A repository for hosting Nextflow configuration files containing custom paramete
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* [Checking user hostnames](#checking-user-hostnames)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs)
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* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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* [Pipeline-specific documentation](#pipeline-specific-documentation)
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* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
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* [Create the pipeline-specific nf-core/configs files](#create-the-pipeline-specific-nf-coreconfigs-files)
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* [Help](#help)
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## Using an existing config
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Currently documentation is available for the following pipeline within the specific profile:
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* ampliseq
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* [BINAC](docs/pipeline/ampliseq/binac.md)
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* eager
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* [SHH](docs/pipeline/eager/shh.md)
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### Enabling pipeline-specific configs within a pipeline
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//Nextflow config file for running on AWS batch
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params {
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config_profile_description = 'AWSBATCH Cloud Profile'
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config_profile_contact = 'Alexander Peltzer (@apeltzer)'
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config_profile_url = 'https://aws.amazon.com/batch/'
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awsqueue = false
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awsregion = 'eu-west-1'
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config_profile_contact = 'Alexander Peltzer (@apeltzer)'
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config_profile_description = 'AWSBATCH Cloud Profile'
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config_profile_name = 'AWSBATCH'
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config_profile_url = 'https://aws.amazon.com/batch/'
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awscli = '/home/ec2-user/miniconda/bin/aws'
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tracedir = './'
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}
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process.executor = 'awsbatch'
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executor.awscli = '/home/ec2-user/miniconda/bin/aws'
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process.queue = params.awsqueue
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aws.region = params.awsregion
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executor.awscli = params.awscli
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singularity {
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enabled = true
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envWhitelist = 'TZ'
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}
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process {
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max_cpus = 32
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max_time = 72.h
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igenomes_base = '/camp/svc/reference/Genomics/iGenomes'
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igenomes_base = '/camp/svc/reference/Genomics/aws-igenomes'
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}
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conf/pipeline/ampliseq/binac.config
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conf/pipeline/ampliseq/binac.config
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// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'Alexander Peltzer (@apeltzer)'
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config_profile_description = 'nf-core/ampliseq BINAC profile provided by nf-core/configs'
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}
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env {
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TZ='Europe/Berlin'
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}
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// Specific nf-core/sarek process configuration
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process {
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withLabel:sentieon {
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if (params.sentieon) {
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module = 'sentieon/201808.05'
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container = null
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}
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module = {params.sentieon ? 'sentieon/201808.05' : null}
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container = {params.sentieon ? null : container}
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}
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}
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# nf-core/configs: awsbatch Configuration
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To be used with `awsbatch`.
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Custom queue and region can be entered with `params.awsqueue` and `params.region` respectively.
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Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.
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```bash
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## Load Nextflow and Singularity environment modules
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module purge
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module load Nextflow/0.32.0
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module load Nextflow/19.10.0
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module load Singularity/2.6.0-foss-2016b
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```
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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).
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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).
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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).
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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).
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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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docs/pipeline/ampliseq/binac.md
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docs/pipeline/ampliseq/binac.md
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# nf-core/configs: binac ampliseq specific configuration
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Extra specific configuration for the ampliseq pipeline.
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## Usage
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To use, run the pipeline with `-profile binac`.
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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.
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Example: `nextflow run nf-core/ampliseq -profile binac`
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## ampliseq specific configurations for binac
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Specific configurations for BINAC has been made for ampliseq.
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* Specifies the `TZ` `ENV` variable to be `Europe/Berlin` to fix a QIIME2 issue
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pipeline/ampliseq.config
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pipeline/ampliseq.config
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/*
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* -------------------------------------------------
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* nfcore/ampliseq custom profile Nextflow config file
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* -------------------------------------------------
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* Config options for custom environments.
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* Cluster-specific config options should be saved
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* in the conf/pipeline/ampliseq folder and imported
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* under a profile name here.
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*/
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profiles {
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binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
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}
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