From d52db660777c4bf36546ddb188ec530c3ada1b96 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 23 Nov 2018 15:56:34 +0000 Subject: [PATCH] Added existing configs from all pipelines --- conf/binac.config | 22 ++++++++++++++++++++++ conf/ccga.config | 25 +++++++++++++++++++++++++ conf/cfc.config | 21 +++++++++++++++++++++ conf/crick.config | 23 +++++++++++++++++++++++ conf/gis.config | 23 +++++++++++++++++++++++ conf/hebbe.config | 26 ++++++++++++++++++++++++++ conf/uct_hex.config | 27 +++++++++++++++++++++++++++ conf/uppmax-devel.config | 24 ++++++++++++++++++++++++ conf/uppmax.config | 28 ++++++++++++++++++++++++++++ conf/uzh.config | 19 +++++++++++++++++++ 10 files changed, 238 insertions(+) create mode 100644 conf/binac.config create mode 100644 conf/ccga.config create mode 100644 conf/cfc.config create mode 100755 conf/crick.config create mode 100644 conf/gis.config create mode 100644 conf/hebbe.config create mode 100644 conf/uct_hex.config create mode 100644 conf/uppmax-devel.config create mode 100644 conf/uppmax.config create mode 100644 conf/uzh.config diff --git a/conf/binac.config b/conf/binac.config new file mode 100644 index 0000000..be69d9e --- /dev/null +++ b/conf/binac.config @@ -0,0 +1,22 @@ +/* + * ---------------------------------------------------------------------------- + * Nextflow config file for use with Singularity on BINAC cluster in Tuebingen + * ---------------------------------------------------------------------------- + * Defines basic usage limits and singularity image id. + */ + +singularity { + enabled = true +} + +process { + beforeScript = 'module load devel/singularity/3.0.1' + executor = 'pbs' + queue = 'short' +} + +params { + max_memory = 128.GB + max_cpus = 28 + max_time = 48.h +} diff --git a/conf/ccga.config b/conf/ccga.config new file mode 100644 index 0000000..bc9959d --- /dev/null +++ b/conf/ccga.config @@ -0,0 +1,25 @@ +/* + * ------------------------------------------------- + * Nextflow config file with environment modules for RZCluster in Kiel + * ------------------------------------------------- + */ + +executor { + queueSize=100 +} + +process { + + // Global process config + executor = 'slurm' + queue = 'ikmb_a' + + clusterOptions = { "--qos=ikmb_a" } + +} + +params { + // illumina iGenomes reference file paths on RZCluster + igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/' + saveReference = true +} diff --git a/conf/cfc.config b/conf/cfc.config new file mode 100644 index 0000000..6285925 --- /dev/null +++ b/conf/cfc.config @@ -0,0 +1,21 @@ +/* + * ------------------------------------------------------------- + * Nextflow config file for use with Singularity on CFC at QBIC + * ------------------------------------------------------------- + * Defines basic usage limits and singularity image id. + */ + +singularity { + enabled = true +} + +process { + beforeScript = 'module load qbic/singularity_slurm/3.0.1' + executor = 'slurm' +} + +params { + max_memory = 60.GB + max_cpus = 24 + max_time = 140.h +} diff --git a/conf/crick.config b/conf/crick.config new file mode 100755 index 0000000..aa356e8 --- /dev/null +++ b/conf/crick.config @@ -0,0 +1,23 @@ +/* + * ------------------------------------------------- + * Nextflow config file for CAMP HPC @ The Crick + * ------------------------------------------------- + */ + +singularity { + enabled = true + autoMounts = true +} + +process { + beforeScript = 'module load Singularity/2.6.0-foss-2016b' + executor = 'slurm' +} + +params { + max_memory = 224.GB + max_cpus = 32 + max_time = 72.h + + igenomes_base = '/camp/svc/reference/Genomics/iGenomes' +} diff --git a/conf/gis.config b/conf/gis.config new file mode 100644 index 0000000..3fcb72e --- /dev/null +++ b/conf/gis.config @@ -0,0 +1,23 @@ +/* + * ------------------------------------------------- + * Nextflow config file for GIS (Aquila) + * ------------------------------------------------- + * Defines reference genomes, using iGenome paths + * Imported under the default 'standard' Nextflow + * profile in nextflow.config + */ + +process { + executor = 'sge' + clusterOptions = { "-l mem_free=" + task.memory.toString().replaceAll(/[\sB]/,'') } + penv = 'OpenMP' + errorStrategy = { task.attempt < 2 ? 'retry' : 'finish' } + // auto translate container name into conda environment name + beforeScript = { 'source /mnt/projects/rpd/rc/init.2017-04; module load miniconda3; set +u; source activate nfcore-rnaseq-1.0dev; set -u;' } +} +params { + saveReference = true + // illumina iGenomes reference file paths on GIS Aquila + igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/' +} + diff --git a/conf/hebbe.config b/conf/hebbe.config new file mode 100644 index 0000000..86f8468 --- /dev/null +++ b/conf/hebbe.config @@ -0,0 +1,26 @@ +/* + * ------------------------------------------------- + * Gothenburg Hebbe Cluster config file + * ------------------------------------------------- + * http://www.c3se.chalmers.se/index.php/Hebbe + */ + + +singularity { + enabled = true +} + +process { + executor = 'slurm' + clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" } + + /* The Hebbe scheduler fails if you try to request an amount of memory for a job */ + withName: '*' { memory = null } +} + +params { + saveReference = true + max_memory = 64.GB + max_cpus = 20 + max_time = 240.h +} diff --git a/conf/uct_hex.config b/conf/uct_hex.config new file mode 100644 index 0000000..422a143 --- /dev/null +++ b/conf/uct_hex.config @@ -0,0 +1,27 @@ +/* + * ------------------------------------------------- + * University of Cape Town HEX cluster config file + * ------------------------------------------------- + * http://hpc.uct.ac.za/index.php/hex-3/ + */ + +singularity { + enabled = true + cacheDir = "/scratch/DB/bio/singularity-containers" +} + +process { + stageInMode = 'symlink' + stageOutMode = 'rsync' + queue = 'UCTlong' + clusterOptions = { "-M $params.email -m abe -l nodes=1:ppn=1:series600" } +} + +executor{ + executor = 'pbs' + jobName = { "$task.tag" } +} + +params { + igenomes_base = '/scratch/DB/bio/rna-seq/references' +} diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config new file mode 100644 index 0000000..c77db4a --- /dev/null +++ b/conf/uppmax-devel.config @@ -0,0 +1,24 @@ +/* + * ------------------------------------------------- + * Nextflow config file for UPPMAX (milou / irma) + * ------------------------------------------------- + * To be applied after main UPPMAX config, overwrites config and + * submits jobs to the `devcore` queue, which has much faster + * queue times. All jobs are limited to 1 hour to be eligible + * for this queue and only one job allowed at a time. + */ + +executor { + name = 'slurm' + queueSize = 1 +} +process { + queue = 'devel' +} + +params { + // Max resources to be requested by a devel job + max_memory = 120.GB + max_cpus = 16 + max_time = 1.h +} diff --git a/conf/uppmax.config b/conf/uppmax.config new file mode 100644 index 0000000..89fbce1 --- /dev/null +++ b/conf/uppmax.config @@ -0,0 +1,28 @@ +/* + * ------------------------------------------------- + * Nextflow config file for UPPMAX (milou / irma) + * ------------------------------------------------- + * Defines reference genomes, using iGenome paths + * Imported under the default 'standard' Nextflow + * profile in nextflow.config + */ + +singularity { + enabled = true +} + +process { + executor = 'slurm' + clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" } +} + +params { + saveReference = true + // Max resources requested by a normal node on milou. If you need more memory, run on a fat node using: + // --clusterOptions "-C mem512GB" --max_memory "512GB" + max_memory = 128.GB + max_cpus = 16 + max_time = 240.h + // illumina iGenomes reference file paths on UPPMAX + igenomes_base = '/sw/data/uppnex/igenomes/' +} diff --git a/conf/uzh.config b/conf/uzh.config new file mode 100644 index 0000000..68cd7dd --- /dev/null +++ b/conf/uzh.config @@ -0,0 +1,19 @@ +/* + * -------------------------------------------------------------------------------- + * Nextflow config file for use with Singularity on University of Zurich Cluster + * -------------------------------------------------------------------------------- + */ + +singularity { + enabled = true +} + +process { + executor = 'slurm' +} + +params { + max_memory = 1800.GB + max_cpus = 112 + max_time = 168.h +}