Optimised settings for minimap2, taken from the read-mapping pipeline

sanger-tol · Mar 22, 2024 · bf82511 · bf82511
1 parent b967b51
commit bf82511
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Showing 4 changed files with 34 additions and 2 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -53,6 +53,26 @@ process {
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }
     }
 
+    withName: '.*:MINIMAP2_ALIGNMENT:MINIMAP2_CCS' {
+        cpus   = { log_increase_cpus(4, 2*task.attempt, meta.read_count/1000000, 2) }
+        memory = { check_max( 800.MB * log_increase_cpus(4, 2*task.attempt, meta.read_count/1000000, 2) + 14.GB * Math.ceil( Math.pow(meta2.genome_size / 1000000000, 0.6)) * task.attempt, 'memory' ) }
+        time   = { check_max(        3.h  * Math.ceil( meta.read_count   / 1000000   ) * task.attempt, 'time'   ) }
+    }
+
+    // Extrapolated from the HIFI settings on the basis of 1 ONT alignment. CLR assumed to behave the same way as ONT
+    withName: '.*:MINIMAP2_ALIGNMENT:MINIMAP2_(CLR|ONT)' {
+        cpus   = { log_increase_cpus(4, 2*task.attempt, meta.read_count/1000000, 2) }
+        memory = { check_max( 800.MB * log_increase_cpus(4, 2*task.attempt, meta.read_count/1000000, 2) + 30.GB * Math.ceil( Math.pow(meta2.genome_size / 1000000000, 0.6)) * task.attempt, 'memory' ) }
+        time   = { check_max(        1.h  * Math.ceil( meta.read_count   / 1000000   ) * task.attempt, 'time'   ) }
+    }
+
+    // Temporarily the same settings as CCS
+    withName: '.*:MINIMAP2_ALIGNMENT:MINIMAP2_(HIC|ILMN)' {
+        cpus   = { log_increase_cpus(4, 2*task.attempt, meta.read_count/1000000, 2) }
+        memory = { check_max( 800.MB * log_increase_cpus(4, 2*task.attempt, meta.read_count/1000000, 2) + 14.GB * Math.ceil( Math.pow(meta2.genome_size / 1000000000, 0.6)) * task.attempt, 'memory' ) }
+        time   = { check_max(        3.h  * Math.ceil( meta.read_count   / 1000000   ) * task.attempt, 'time'   ) }
+    }
+
     withName: 'WINDOWSTATS_INPUT' {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         // 2 GB per 1 Gbp

diff --git a/modules.json b/modules.json
@@ -56,7 +56,8 @@
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "2c2d1cf80866dbd6dd0ea5d61ddd59533a72d41e",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
                     "multiqc": {
                         "branch": "master",

diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf
diff --git a/modules/nf-core/minimap2/align/minimap2-align.diff b/modules/nf-core/minimap2/align/minimap2-align.diff