configs

configs/container.config

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+process {
+    withLabel:  ubuntu      { container = 'nanozoo/template:3.8--e13dfeb' }
+    withLabel:  bakta       { container = 'nanozoo/bakta:1.2.1--bf38720' } 
+    withLabel:  prokka      { container = 'nanozoo/prokka:1.14.6--c99ff65'}
+    withLabel:  eggnog      { container = 'nanozoo/eggnog-mapper:2.1.9--4f2b6c0' }
+    }

configs/local.config

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+process.executor = 'local'
+
+process {
+    withLabel:  ubuntu      { cpus = 1 }
+    withLabel:  prokka      { cpus = params.cores }
+    withLabel:  bakta       { cpus = params.cores } 
+    withLabel:  eggnog      { cpus = params.cores } 
+    }

configs/nodes.config

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+process {
+    withLabel:  ubuntu      { cpus = 2; memory = '2 GB' }
+    withLabel:  bakta       { cpus = 8; memory = '16 GB' }
+    withLabel:  prokka      { cpus = 8; memory = '16 GB' }
+    withLabel:  eggnog      { cpus = 8; memory = '16 GB' }
+    }

nextflow.config

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+manifest {
+    mainScript = 'main.nf'
+    name = 'anno_bench'
+}
+
+// default parameters
+params {
+    cores = Runtime.runtime.availableProcessors().intdiv(4)
+    help = false
+    max_cores = Runtime.runtime.availableProcessors()
+    memory = '12'
+    profile = false
+
+// inputs
+    fasta = ''
+
+// settings
+
+
+// folder structure
+	output = "results"
+	runinfodir = "Runinfo"
+
+
+}
+
+
+// runinfo
+timeline {
+  enabled = true
+  file = "${params.output}/${params.runinfodir}/execution_timeline.html"
+}
+
+report {
+  enabled = true
+  file = "${params.output}/${params.runinfodir}/execution_report.html"
+}
+
+
+profiles {
+    local {
+        workDir = "work/nextflow-anno_bench-$USER"
+        includeConfig 'configs/local.config'
+        executor {
+            name = "local"
+            cpus = params.max_cores
+            memory = params.memory
+        }
+
+        process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'terminate' }
+    }
+
+
+    docker {
+        docker { enabled = true }
+        includeConfig 'configs/container.config'
+    }
+
+    stub {
+        params.max_cores = 2
+        params.cores = 2
+    }
+
+
+    ukj_cloud { 
+    workDir = "/tmp/nextflow-anno_bench-$USER"
+    docker { enabled = true }
+    process.executor = 'google-lifesciences'
+    params.databases = 'gs://persistant-storage/poreCov/'
+    bucketDir = 'gs://case-tmp-dir/anno_bench/'
+    google {  
+        project = 'case-dev-302214'
+        zone = 'europe-west1-b,europe-west1-c,europe-west2-b,europe-west2-a'
+        lifeSciences.preemptible = true
+        lifeSciences.bootDiskSize = 20.GB
+        }
+    includeConfig 'configs/container.config'
+    includeConfig 'configs/nodes.config'
+
+    // cloud error strategy
+    process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'ignore' }
+    process.maxRetries = 3
+    }
+
+// test_profile
+//    test {
+//    }
+}