Resources review

sanger-tol · Nov 21, 2024 · 8356733 · 8356733
1 parent f7d9db2
commit 8356733
Showing 1 changed file with 14 additions and 3 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -88,6 +88,7 @@ process {
     withName:SAMTOOLS_MERGE {
         cpus    = { check_max( 16        * 1, 'cpus'  ) }
         memory  = { check_max( 50.GB     * task.attempt, 'memory') }
+        time    = { check_max( 30.h     * task.attempt, 'time') }
     }
 
     // RESOURCES: MEMORY INTENSIVE STEPS, SOFTWARE TO BE UPDATED TO COMBAT THIS
@@ -163,7 +164,7 @@ process {
     }
     withName: CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
         cpus    = { check_max( 16       * 1                                                 , 'cpus'   ) }
-        memory  = { check_max( 1.GB     * ( reference.size() < 2e9 ? 50 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
+        memory  = { check_max( 1.GB     * ( reference.size() < 2e9 ? 80 : Math.ceil( ( reference.size() / 1e+9 ) * 30 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
     }
 
     withName: CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
@@ -179,11 +180,13 @@ process {
     withName: PRETEXTMAP_STANDRD{
         cpus    = { check_max( 8       * 1, 'cpus'   ) }
         memory  = { check_max( 3.GB     * task.attempt, 'memory' ) }
+        time   =  { check_max( 1.h      * ( ( fasta.size() < 4e9 ? 24 : 48 ) * Math.ceil( task.attempt * 1 ) ), 'time'    ) }
     }
 
     withName: PRETEXTMAP_HIGHRES {
         cpus    = { check_max( 6       * task.attempt, 'cpus'   ) }
         memory  = { check_max( 20.GB     * Math.ceil( task.attempt * 2.6 ), 'memory' ) }
+        time   =  { check_max( 1.h      * ( ( fasta.size() < 4e9 ? 24 : 48 ) * Math.ceil( task.attempt * 1 ) ), 'time'    ) }
     }
 
     withName: PRETEXT_GRAPH {
@@ -207,7 +210,8 @@ process {
     // add a cpus 16 if bam.size() >= 50GB
     withName: BAMTOBED_SORT {
         cpus    = { check_max( 12     * 1, 'cpus'    ) }
-        memory  = { check_max( 3.GB * Math.ceil( bam.size() / 1e+9 ) * task.attempt, 'memory'  ) }
+        memory  =  { check_max( 1.GB * ( ( bam.size() < 150e9 ? Math.ceil( bam.size() / 1e+9 ) : Math.ceil( bam.size() / 4e+9 ) ) * Math.ceil( task.attempt * 1 ) ), 'memory'    ) }
+        time    = { check_max( 30.h      * task.attempt, 'time'    ) }
     }
 
     withName: SAMTOOLS_MARKDUP {
@@ -217,7 +221,7 @@ process {
 
     withName: COOLER_CLOAD {
         cpus   = { check_max( 16        * 1, 'cpus'    ) }
-        memory = { check_max( 6.GB      * task.attempt, 'memory'  ) }
+        memory = { check_max( 20.GB      * task.attempt, 'memory'  ) }
     }
 
     withName: MERQURYFK_MERQURYFK {
@@ -278,6 +282,7 @@ process {
     withName: GET_PAIRED_CONTACT_BED {
         cpus   = { check_max( ${ file.size() > 1e11 ? 12 : 6 }  , 'cpus'    ) }
         memory = { check_max( 1.GB      * Math.ceil( file.size() / 2e+9 )  * task.attempt  , 'memory'  ) }
+        time    = { check_max( 30.h      * task.attempt, 'time'    ) }
     }
 
     //
@@ -308,4 +313,10 @@ process {
     withName: BEDTOOLS_INTERSECT {
         memory  = { check_max( 6.GB     * (task.attempt * task.attempt), 'memory'    ) }
     }
+
+    withName: GENERATE_CRAM_CSV {
+        cpus   = { check_max( 6                         , 'cpus'    ) }
+        memory = { check_max( 30.GB      * task.attempt , 'memory'  ) }
+        time   = { check_max( 10.h      * task.attempt  , 'time'    ) }
+    }
 }