Merge pull request #47 from hoelzer/dev

Dev
hoelzer · Sep 30, 2020 · 7f12d99 · 7f12d99
2 parents 67c2918 + 47eaf9a
commit 7f12d99
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Showing 4 changed files with 21 additions and 12 deletions.
diff --git a/configs/node.config b/configs/node.config
@@ -2,8 +2,8 @@ process {
         withLabel: basics {     cpus = 2 ;  memory = '16 GB' }
         withLabel: bbmap {      cpus = 24 ; memory = '16 GB' }
         withLabel: fastp {      cpus = 12 ; memory = '16 GB' }
-        withLabel: prodigal {   cpus = 8 ;  memory = '16 GB' }
-        withLabel: diamond {    cpus = 12 ; memory = '16 GB' }
+        withLabel: prodigal {   cpus = 1 ;  memory = '4 GB' }
+        withLabel: diamond {    cpus = 24 ; memory = '16 GB' }
         withLabel: ggplot2 {    cpus = 2 ;  memory = '4 GB' }
         withLabel: nanoplot {   cpus = 8 ;  memory = '14 GB' }
         withLabel: spades {     cpus = 32 ; memory = '80 GB' }

diff --git a/main.nf b/main.nf
@@ -93,6 +93,7 @@ if (params.host) {
     .view()
 }
 
+
 /************************** 
 * MODULES
 **************************/

diff --git a/modules/spades.nf b/modules/spades.nf
@@ -2,19 +2,19 @@ process spades {
     label 'spades'
     publishDir "${params.output}/${name}/assembly/", mode: 'copy', pattern: "${name}_raw_assembly.fasta"
 
-    errorStrategy { 'retry' }
-    cpus { 36 }
-    memory { 400.GB * task.attempt }
-    clusterOptions { '-P bigmem' }
-    maxRetries 3
-
     input:
         tuple val(name), file(ont), file(illumina)
     output:
         tuple val(name), file("${name}_raw_assembly.fasta")
     script:
         """
-        MEM=\$(echo ${task.memory} | sed 's/ GB//g')
+	SIZE=\$(echo ${task.memory} | awk 'BEGIN{FS=" "};{print \$2}')
+	if [ \$SIZE == "TB" ]; then
+          MEM=\$(echo ${task.memory} | sed 's/ TB//g') 
+	  MEM=\$(echo \$MEM*1000 | bc | awk 'BEGIN{FS="."};{print \$1}')
+	else
+          MEM=\$(echo ${task.memory} | sed 's/ GB//g') 
+	fi
         spades.py --only-assembler -1 ${illumina[0]} -2 ${illumina[1]} --nanopore ${ont} --meta -o spades_output -t ${task.cpus} -m \${MEM}
         mv spades_output/contigs.fasta  ${name}_raw_assembly.fasta
         """

diff --git a/nextflow.config b/nextflow.config
@@ -175,11 +175,15 @@ profiles {
         }
         includeConfig 'configs/container.config' 
 
+
         /*
-        process {
+	process {
             withLabel: spades { cpus = 32;
-                                memory = '200 GB';
-                                clusterOptions = '-P bigmem' }
+                                memory = 90.GB * task.attempt;
+                                clusterOptions = '-P bigmem'; 
+                                errorStrategy { task.exitStatus in 130..140 ? 'retry' : 'terminate' };
+				maxRetries 4 }
+	
             withLabel: flye {   cpus = 30; 
                                 memory { 120.GB * task.attempt };
                                 clusterOptions = '-P bigmem';
@@ -209,6 +213,10 @@ profiles {
                 cacheDir = params.cachedir
         }
         includeConfig 'configs/container.config' 
+
+        process {
+            withLabel: spades { cpus = 32; memory = {1600.GB * task.attempt}; clusterOptions = '-P bigmem'; errorStrategy = { task.exitStatus in 1 || 130..140 ? 'retry' : 'terminate' }; maxRetries = 4; }
+	}
     }
 
     ara {