Add bactmap_update_global_use.config file

pipeline/bactmap_update_global_use.config

@@ -0,0 +1,138 @@
+/*
+ * =========================
+ *  GLOBAL DEFAULT SETTINGS
+ * =========================
+ */
+
+params {
+
+  /*
+   * Execution behaviour
+   */
+  fail_fast            = false        // true = stop on first error
+  skip_samples_on_fail = true
+  exclude_samples      = []
+
+  /*
+   * Resource caps (global maximums)
+   */
+  max_cpus   = 64
+  max_memory = 250.GB
+  max_time   = 24.h
+
+  /*
+   * Logging
+   */
+  log_dir = 'logs'
+}
+
+
+/*
+ * =========================
+ *  PROCESS DEFAULTS
+ * =========================
+ */
+
+process {
+
+  errorStrategy = params.fail_fast ? 'terminate' : 'ignore'
+  maxRetries    = 0
+  maxErrors     = -1
+
+  /*
+   * Resource requests
+   * Individual processes can still override these
+   */
+  cpus   { Math.min(64, params.max_cpus) }
+  memory { params.max_memory }
+  time   { params.max_time }
+
+  scratch        = true
+  publishDirMode = 'copy'
+}
+
+
+/*
+ * =========================
+ *  CONTAINER SUPPORT
+ * =========================
+ */
+
+singularity {
+  enabled      = true
+  autoMounts   = true
+  pullTimeout  = '4h'
+
+  /*
+   * Use env var if set, otherwise default to work directory
+   * Works across users and systems
+   */
+  cacheDir = "${System.getenv('NXF_SINGULARITY_CACHEDIR') ?: "$baseDir/.singularity"}"
+}
+
+
+/*
+ * =========================
+ *  PIPELINE REPORTING
+ * =========================
+ */
+
+timeline {
+  enabled   = true
+  file      = "${params.log_dir}/timeline.html"
+  overwrite = true
+}
+
+trace {
+  enabled   = true
+  file      = "${params.log_dir}/trace.txt"
+  overwrite = true
+}
+
+report {
+  enabled   = true
+  file      = "${params.log_dir}/report.html"
+  overwrite = true
+}
+
+dag {
+  enabled   = true
+  file      = "${params.log_dir}/flowchart.png"
+  overwrite = true
+}
+
+
+/*
+ * =========================
+ *  EXECUTION PROFILES
+ * =========================
+ */
+
+profiles {
+
+  /*
+   * Default: safe for most systems
+   */
+  standard {
+    process.executor = 'local'
+  }
+
+  /*
+   * Local workstation / laptop
+   */
+  local {
+    process.executor = 'local'
+    params.max_cpus   = 8
+    params.max_memory = 32.GB
+    params.max_time   = 6.h
+  }
+
+  /*
+   * HPC / scheduler-based systems
+   */
+  hpc {
+    process.executor = 'slurm'   // change if needed (pbs, lsf, sge)
+    process.queue    = 'standard'
+    process.clusterOptions = '--export=ALL'
+  }
+}