diff 0.2.1/conf/modules.config @ 0:77494b0fa3c7

"planemo upload"
author kkonganti
date Mon, 27 Jun 2022 15:55:37 -0400
parents
children 1cb92deb15f8
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.1/conf/modules.config	Mon Jun 27 15:55:37 2022 -0400
@@ -0,0 +1,87 @@
+process {
+    publishDir = [
+        path: { 
+            "${task.process.tokenize(':')[-1].toLowerCase()}" == "multiqc" ?
+                "${params.output}${params.fs}${params.pipeline.toLowerCase()}-${task.process.tokenize(':')[-1].toLowerCase()}" :
+                "${params.output}${params.fs}${task.process.tokenize(':')[-1].toLowerCase()}"
+        },
+        mode: params.publish_dir_mode,
+        overwrite: params.publish_dir_overwrite,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    errorStrategy = {
+        ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 1000) : 'finish'
+    }
+
+    maxRetries = 11
+
+    withLabel: 'process_femto' {
+        cpus= 1
+    }
+
+    withLabel: 'process_pico' {
+        cpus= 2
+    }
+
+    withLabel: 'process_nano' {
+        cpus= 4
+    }
+
+    withLabel: 'process_micro' {
+        cpus= 8
+    }
+
+    withLabel: 'process_only_mem_low' {
+        cpus= 1
+    }
+
+    withLabel: 'process_only_mem_medium' {
+        cpus= 1
+    }
+
+    withLabel: 'process_only_mem_high' {
+        cpus= 1
+    }
+
+    withLabel: 'process_low' {
+        cpus= 10
+    }
+
+    withLabel: 'process_medium' {
+        cpus= 10
+    }
+
+    withLabel: 'process_high' {
+        cpus= 10
+    }
+
+    withLabel: 'process_higher' {
+        cpus= 10
+    }
+
+    withLabel: 'process_gigantic' {
+        cpus= 10
+    }
+}
+
+if ( (params.input || params.metadata ) && params.pipeline ) {
+    try {
+        includeConfig "${params.workflowsconf}${params.fs}process${params.fs}${params.pipeline}.process.config"
+    } catch (Exception e) {
+        System.err.println('-'.multiply(params.linewidth) + "\n" +
+            "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
+            '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
+            "default pipeline's process configuration. Please provide a pipeline \n" +
+            "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
+        System.exit(1)
+    }
+}
+
+// Function will return after sleeping for some time. 
+// Sleep time increases exponentially by tast attempt.
+def dynamic_retry(task_retry_num, factor_by) {
+    println tas
+    sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
+    return 'retry'
+}
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