mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
Added existing configs from all pipelines
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10 changed files with 238 additions and 0 deletions
22
conf/binac.config
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22
conf/binac.config
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/*
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* ----------------------------------------------------------------------------
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* Nextflow config file for use with Singularity on BINAC cluster in Tuebingen
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* ----------------------------------------------------------------------------
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* Defines basic usage limits and singularity image id.
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*/
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singularity {
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enabled = true
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}
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process {
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beforeScript = 'module load devel/singularity/3.0.1'
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executor = 'pbs'
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queue = 'short'
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}
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params {
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max_memory = 128.GB
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max_cpus = 28
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max_time = 48.h
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}
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25
conf/ccga.config
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conf/ccga.config
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/*
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* -------------------------------------------------
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* Nextflow config file with environment modules for RZCluster in Kiel
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* -------------------------------------------------
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*/
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executor {
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queueSize=100
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}
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process {
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// Global process config
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executor = 'slurm'
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queue = 'ikmb_a'
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clusterOptions = { "--qos=ikmb_a" }
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}
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params {
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// illumina iGenomes reference file paths on RZCluster
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igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/'
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saveReference = true
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}
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21
conf/cfc.config
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21
conf/cfc.config
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/*
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* -------------------------------------------------------------
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* Nextflow config file for use with Singularity on CFC at QBIC
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* -------------------------------------------------------------
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* Defines basic usage limits and singularity image id.
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*/
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singularity {
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enabled = true
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}
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process {
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beforeScript = 'module load qbic/singularity_slurm/3.0.1'
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executor = 'slurm'
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}
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params {
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max_memory = 60.GB
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max_cpus = 24
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max_time = 140.h
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}
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23
conf/crick.config
Executable file
23
conf/crick.config
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/*
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* -------------------------------------------------
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* Nextflow config file for CAMP HPC @ The Crick
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* -------------------------------------------------
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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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process {
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beforeScript = 'module load Singularity/2.6.0-foss-2016b'
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executor = 'slurm'
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}
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params {
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max_memory = 224.GB
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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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}
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23
conf/gis.config
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conf/gis.config
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/*
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* -------------------------------------------------
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* Nextflow config file for GIS (Aquila)
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* -------------------------------------------------
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* Defines reference genomes, using iGenome paths
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* Imported under the default 'standard' Nextflow
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* profile in nextflow.config
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*/
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process {
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executor = 'sge'
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clusterOptions = { "-l mem_free=" + task.memory.toString().replaceAll(/[\sB]/,'') }
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penv = 'OpenMP'
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errorStrategy = { task.attempt < 2 ? 'retry' : 'finish' }
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// auto translate container name into conda environment name
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beforeScript = { 'source /mnt/projects/rpd/rc/init.2017-04; module load miniconda3; set +u; source activate nfcore-rnaseq-1.0dev; set -u;' }
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}
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params {
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saveReference = true
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// illumina iGenomes reference file paths on GIS Aquila
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igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/'
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}
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26
conf/hebbe.config
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conf/hebbe.config
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/*
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* -------------------------------------------------
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* Gothenburg Hebbe Cluster config file
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* -------------------------------------------------
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* http://www.c3se.chalmers.se/index.php/Hebbe
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*/
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singularity {
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enabled = true
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}
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process {
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executor = 'slurm'
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clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
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/* The Hebbe scheduler fails if you try to request an amount of memory for a job */
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withName: '*' { memory = null }
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}
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params {
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saveReference = true
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max_memory = 64.GB
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max_cpus = 20
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max_time = 240.h
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}
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27
conf/uct_hex.config
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conf/uct_hex.config
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/*
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* -------------------------------------------------
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* University of Cape Town HEX cluster config file
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* -------------------------------------------------
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* http://hpc.uct.ac.za/index.php/hex-3/
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*/
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singularity {
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enabled = true
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cacheDir = "/scratch/DB/bio/singularity-containers"
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}
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process {
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stageInMode = 'symlink'
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stageOutMode = 'rsync'
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queue = 'UCTlong'
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clusterOptions = { "-M $params.email -m abe -l nodes=1:ppn=1:series600" }
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}
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executor{
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executor = 'pbs'
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jobName = { "$task.tag" }
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}
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params {
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igenomes_base = '/scratch/DB/bio/rna-seq/references'
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}
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24
conf/uppmax-devel.config
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24
conf/uppmax-devel.config
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/*
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* -------------------------------------------------
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* Nextflow config file for UPPMAX (milou / irma)
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* -------------------------------------------------
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* To be applied after main UPPMAX config, overwrites config and
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* submits jobs to the `devcore` queue, which has much faster
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* queue times. All jobs are limited to 1 hour to be eligible
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* for this queue and only one job allowed at a time.
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*/
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executor {
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name = 'slurm'
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queueSize = 1
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}
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process {
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queue = 'devel'
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}
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params {
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// Max resources to be requested by a devel job
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max_memory = 120.GB
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max_cpus = 16
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max_time = 1.h
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}
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28
conf/uppmax.config
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28
conf/uppmax.config
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/*
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* -------------------------------------------------
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* Nextflow config file for UPPMAX (milou / irma)
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* -------------------------------------------------
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* Defines reference genomes, using iGenome paths
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* Imported under the default 'standard' Nextflow
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* profile in nextflow.config
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*/
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singularity {
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enabled = true
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}
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process {
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executor = 'slurm'
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clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
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}
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params {
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saveReference = true
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// Max resources requested by a normal node on milou. If you need more memory, run on a fat node using:
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// --clusterOptions "-C mem512GB" --max_memory "512GB"
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max_memory = 128.GB
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max_cpus = 16
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max_time = 240.h
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// illumina iGenomes reference file paths on UPPMAX
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igenomes_base = '/sw/data/uppnex/igenomes/'
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}
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19
conf/uzh.config
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19
conf/uzh.config
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/*
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* --------------------------------------------------------------------------------
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* Nextflow config file for use with Singularity on University of Zurich Cluster
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* --------------------------------------------------------------------------------
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*/
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singularity {
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enabled = true
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}
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process {
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executor = 'slurm'
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}
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params {
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max_memory = 1800.GB
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max_cpus = 112
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max_time = 168.h
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}
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