Added existing configs from all pipelines

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
+}

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
+}

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
+}

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'
+}

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/'
+}
+

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
+}

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'
+}

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
+}

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/'
+}

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
+}