Xref Mapping New pipeline

nextflow/config/xref.config

@@ -14,15 +14,24 @@ params.sources_config_file = "${params.work_dir}/ensembl-production/src/python/e
 params.source_db_url = ''
 params.skip_download = 0
 params.reuse_db = 0
-params.skip_preparse = 1
-params.split_files_by_species = 1
 params.tax_ids_file = ''
+params.tax_ids_list = ''
 params.update_mode = 0
 
 params.base_path = ''
 params.clean_files = 1
 params.clean_dir = "${params.base_path}/clean_files"
 
+params.species = ''
+params.antispecies = ''
+params.division = ''
+params.run_all = 0
+
+params.history_file = ''
+params.dc_config_file = ''
+params.old_server_uri = ''
+params.registry_file = ''
+
 trace {
     enabled = true
     file = "trace"
@@ -36,50 +45,51 @@ report {
 }
 
 profiles {
+    slurm {
+        process {
+            executor = 'slurm'
+            queue = 'production'
+            queueSize = 300
+            time = '1d'
+            memory = 100.MB
 
-  lsf {
-   process {
-    errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
-    executor = 'lsf'
-    queue = 'production'
-    queueSize = 100
-    maxRetries = 3
-     withLabel:small_process {
-        memory = 200.MB
-        //very specific to lsf
-        executor.perTaskReserve = 200.MB
-    }
-    withLabel: dm {
-        queue = 'datamover'
-        time = '2h'
-    }
-  }
- }
-
-  slurm {
-   process {
-    errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
-    executor = 'slurm'
-    queue = 'production'
-    queueSize = 100
-    maxRetries = 3
-    time = '1d'
-
-    withLabel:small_process {
-        memory = 200.MB
-    }
+            errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
+            maxRetries = 2
 
-    withLabel: dm {
-        queue = 'datamover'
-        time = '3h'
-        memory = 2.GB
-    }
-    withLabel:mem4GB {
-        time = '5d'
-        memory = 4.GB
-    }
-  }
- }
-}
+            withLabel:small_process {
+                memory = 200.MB
+            }
+
+            withLabel:dm {
+                queue = 'datamover'
+                memory = 2.GB
+            }
+
+            withLabel:mem1GB {
+                memory = 1.GB
+            }
+
+            withLabel: mem10GB {
+                memory = 10.GB
+            }
 
+            withLabel:cleanup_mem {
+                memory = 4.GB
+                errorStrategy = 'retry'
+                maxRetries = 0
+                time = '7d'
+            }
 
+            withLabel:align_mem {
+                errorStrategy = 'retry'
+                maxRetries = 5
+                memory = { task.attempt <= 5 ? 4.GB * (task.attempt * task.attempt) : 16.GB  }
+            }
+
+            withLabel:mapping_mem {
+                memory = 4.GB
+                maxRetries = 0
+            }
+        }
+    }
+}