moved config

nextflow.config

@@ -0,0 +1,137 @@
+/* 
+ See the NOTICE file distributed with this work for additional information
+ regarding copyright ownership.
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Default config options for all compute environments
+----------------------------------------------------------------------------------------
+*/
+
+// Set minimum required Nextflow version, stopping execution if current version does not match
+nextflowVersion = '!>=23.01'
+
+// Global default params, used in configs
+params {
+  // Input options
+
+
+  // db connection 
+  username = 'username'
+  password = 'password'
+  transcriptomic_dbname  = ''               
+  transcriptomic_dbhost = ''                  
+  transcriptomic_dbport = ''  
+  transcriptomic_dbuser = ''   
+  transcriptomic_dbpassword = '' 
+
+  ftpBaseUrl="ftp://ftp.sra.ebi.ac.uk/vol1/fastq"
+  ncbiBaseUrl="https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/"
+
+
+
+  enscode = ''
+  bioperl = "${params.enscode}/bioperl-1.6.924"
+
+  help = false
+  cleanCache = false
+  //outDir='/hps/nobackup/flicek/ensembl/genebuild/transcriptomic_assessment/metadata_qc'
+  outDir=''
+  cacheDir = "${params.outDir}/cache"
+  files_latency = '60'
+}
+
+env {
+  ENSCODE = "${params.enscode}"
+  PERL5LIB = "${params.enscode}/ensembl/modules:${params.enscode}/ensembl-analysis/modules:${params.enscode}/ensembl-anno/:" +
+    "${params.enscode}/ensembl-io/modules:${params.bioperl}:$PERL5LIB"
+}
+
+scratch = ''
+workDir = ''
+
+
+singularity {
+  enabled = true
+  autoMounts = true
+  pullTimeout = '1 hour'
+}
+
+profiles {
+
+  standard {
+    executor {
+      name = 'lsf'
+      perJobMemLimit = true
+      queueSize = 2000
+      submitRateLimit = "10/1sec"
+      queueGlobalStatus = true
+      exitReadTimeout = "30 min"
+    }
+
+    process {
+      queue = 'production'
+    }
+  }
+
+  slurm {
+    executor {
+      name = 'slurm'
+      queueSize = 2000
+      submitRateLimit = "10/1sec"
+      queueGlobalStatus = true
+      exitReadTimeout = "30 min"
+    }
+
+    process {
+      clusterOptions = '-t 7-00:00:00 -e errlog.txt'
+    }
+  }
+
+  local {
+    process.executor = 'local'
+  }
+
+}
+
+process {
+  errorStrategy = { task.exitStatus in [104, 137, 140, 143] ? 'retry' : 'terminate' }
+  maxRetries = 3
+  cache = 'lenient'
+
+  withLabel: 'default' {
+    cpus = 1
+    memory = { 6.GB * task.attempt }
+    time = { 1.h * task.attempt }
+    afterScript = { "sleep 60" }
+    storeDir = { "${params.outDir}/cache/${task.process.tokenize(':')[-1].toLowerCase()}/${task.tag}" }
+  }
+
+  withLabel: 'fastqc' {
+    cpus=10
+    memory = { 5.GB * task.attempt }
+    time = { 4.h * task.attempt }
+    container = "staphb/fastqc:latest"
+  }
+  withLabel: 'fetch_file' {
+    cpus = 1
+    memory = { 8.GB * task.attempt }
+    time = { 2.h * task.attempt }
+  }
+}
+