update requirements for rnafusion v.3

nf-core · Nov 23, 2023 · 5f99339 · 5f99339
1 parent e3f1f78
commit 5f99339
Showing 1 changed file with 21 additions and 21 deletions.
diff --git a/conf/pipeline/rnafusion/hasta.config b/conf/pipeline/rnafusion/hasta.config
@@ -14,11 +14,6 @@ process {
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
         cpus = 1
     }
-    withName:'MEGAFUSION' {
-        memory = { check_max( 500.MB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
-        cpus = 2
-    }
     withName:'MULTIQC' {
         memory = { check_max( 1.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
@@ -34,11 +29,6 @@ process {
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
         cpus = 1
     }
-    withName:'SAMTOOLS_INDEX_FOR_QC' {
-        memory = { check_max( 500.MB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
-        cpus = 2
-    }
     withName:'SAMTOOLS_INDEX_FOR_STARFUSION' {
         memory = { check_max( 500.MB * task.attempt, 'memory'  ) }
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
@@ -54,14 +44,6 @@ process {
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
         cpus = 1
     }
-    withName:'QUALIMAP_RNASEQ' {
-        memory = { check_max( 30.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 24.h  * task.attempt, 'time'    ) }
-        cpus = 1
-    }
-    withName:'QUALIMAP_RNASEQ' {
-        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
-    }
     withName:'ARRIBA' {
         memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 8.h  * task.attempt, 'time'    ) }
@@ -72,12 +54,12 @@ process {
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
         cpus = 2
     }
-    withName:'PICARD_MARKDUPLICATES' {
-        memory = { check_max( 90.GB * task.attempt, 'memory'  ) }
+    withName:'GATK4_MARKDUPLICATES' {
+        memory = { check_max( 65.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 6.h  * task.attempt, 'time'    ) }
         cpus = 6
     }
-    withName:'PICARD_MARKDUPLICATES' {
+    withName:'GATK4_MARKDUPLICATES' {
         clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
     }
     withName:'PICARD_COLLECTRNASEQMETRICS' {
@@ -88,6 +70,14 @@ process {
     withName:'PICARD_COLLECTRNASEQMETRICS' {
         clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
     }
+    withName:'PICARD_COLLECTINSERTSIZEMETRICS' {
+        memory = { check_max( 30.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 6.h  * task.attempt, 'time'    ) }
+        cpus = 2
+    }
+    withName:'PICARD_COLLECTINSERTSIZEMETRICS' {
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
+    }
     withName:'FASTQC_FOR_FASTP' {
         memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 4.h  * task.attempt, 'time'    ) }
@@ -133,4 +123,14 @@ process {
         time   = { check_max( 24.h  * task.attempt, 'time'    ) }
         cpus = 12
     }
+    withName:'AGAT_CONVERTSPGFF2TSV' {
+        memory = { check_max( 1.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus = 1
+    }
+    withName:'VCF_COLLECT' {
+        memory = { check_max( 1.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus = 2
+    }
 }