Merge branch 'master' into gis-branch
Alexander Peltzer
2 years ago
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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 = 'Edmund Miller(@emiller88)'
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config_profile_description = 'nf-core/demultiplex AWS Tower profile provided by nf-core/configs'
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}
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aws {
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batch {
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maxParallelTransfers = 24
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maxTransferAttempts = 3
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}
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client {
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maxConnections = 24
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uploadMaxThreads = 24
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maxErrorRetry = 3
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socketTimeout = 3600000
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uploadRetrySleep = 1000
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uploadChunkSize = 32.MB
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}
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}
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process {
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withName: BASES2FASTQ {
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cpus = 16
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memory = 48.GB
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}
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}
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params {
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config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.'
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config_profile_contact = 'Giuseppe Martone (@giusmar)'
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config_profile_url = 'https://github.com/giusmar'
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}
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process.executor = 'slurm'
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google.zone = 'europe-west1'
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = 'work/singularity'
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}
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params {
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config_profile_description = 'University College London Myriad cluster'
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config_profile_contact = 'Chris Wyatt (ucbtcdr@ucl.ac.uk)'
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config_profile_url = 'https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/'
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}
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process {
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executor='sge'
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penv = 'smp'
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}
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params {
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// Defaults only, expecting to be overwritten
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max_memory = 128.GB
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max_cpus = 36
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max_time = 72.h
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// igenomes_base = 's3://ngi-igenomes/igenomes/'
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}
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// optional executor settings
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executor {
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queueSize = 10
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submitRateLimit = '1 sec'
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}
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singularity {
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enabled = true
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autoMounts = true
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}
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# nf-core/configs: AWS Tower Demultiplex specific configuration
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Extra specific configuration for demultiplex pipeline
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## Usage
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To use, run the pipeline with `-profile aws_tower`.
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This will download and launch the demultiplex specific [`aws_tower.config`](../../../conf/pipeline/demultiplex/aws_tower.config) which has been pre-configured with a setup suitable for AWS batch through tower.
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Example: `nextflow run nf-core/demultiplex -profile aws_tower`
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## eager specific configurations for eva
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Specific configurations for AWS has been made for demultiplex.
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### General profiles
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- The general AWS Tower profile runs with default nf-core/demultiplex parameters, but with modifications to account file transfer speed and optimized bases2fastq resources.
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# nf-core/configs: TIGEM configuration
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To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster.
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---
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This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.
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# nf-core/configs: Myriad Configuration
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All nf-core pipelines have been successfully configured for use on UCL's myriad cluster [University College London](https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/).
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To use, run the pipeline with `-profile ucl_myriad`. This will download and launch the [`ucl_myriad.config`](../conf/ucl_myriad.config) which has been pre-configured with a setup suitable for the myriad cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
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## Using Nextflow on Myriad
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Before running the pipeline you will need to install and configure Nextflow and Singularity.
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### Singularity
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This can be done with the following commands:
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```bash
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## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also
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module add java/openjdk-11/11.0.1
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module add singularity-env/1.0.0
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```
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Then set the correct configuration of the cache directories, where <YOUR_ID> is replaced with you credentials which you can find by entering `whoami` into the terminal once you are logged into myriad. Once you have added your credentials save these lines into your .bashrc file in the base directory (e.g. /home/<YOUR_ID>/.bashrc):
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```bash
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# Set all the Singularity cache dirs to Scratch
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export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/
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export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp
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export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache
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export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull
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# Bind your Scratch directory so it is accessible from inside the container
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export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>
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```
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### Nextflow
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Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (https://github.com/nextflow-io/nextflow/releases), you can then manually set this by entering (`NXF_VER=XX.XX.X`).
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```bash
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## Download Nextflow-all
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curl -s https://get.nextflow.io | bash
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NXF_VER=22.10.0
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nextflow -self-update
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chmod a+x nextflow
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mv nextflow ~/bin/nextflow
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```
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Then make sure that your bin PATH is executable, by placing the following line in your .bashrc:
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```bash
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export PATH=$PATH:/home/<YOUR_ID>/bin
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```
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@ -0,0 +1,13 @@
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/*
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* -------------------------------------------------
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* nfcore/demultiplex custom profile Nextflow config file
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* -------------------------------------------------
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* Config options for custom environments.
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* Cluster-specific config options should be saved
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* in the conf/pipeline/demultiplex folder and imported
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* under a profile name here.
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*/
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profiles {
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aws_tower { includeConfig "${params.custom_config_base}/conf/pipeline/demultiplex/aws_tower.config" }
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}
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