Tweak resources and fix in toulligQC (#5)

Tweak resources
Handle space in toulligQC report title

subworkflows/quality_check.nf

@@ -22,9 +22,9 @@ process fastQC {
   label 'fastqc'
   tag { name }
   publishDir "${params.output_dir}/qc/fastqc", mode: 'copy'
-  cpus { 4 * task.attempt }
-  memory { 8.GB * task.attempt }
-  errorStrategy 'retry'
+  cpus { task.attempt == 1 ? 4 : 8 }
+  memory { 4.GB * (Math.pow(2, task.attempt - 1)) }
+  errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'finish' }
   maxRetries 3
 
   when:
@@ -42,7 +42,8 @@ process fastQC {
   fastqc \
     ${reads} \
     -o fastqc_${name} \
-    -t ${task.cpus} --memory ${task.memory.toGiga()}GB
+    -t ${task.cpus} \
+    --memory ${task.memory.toMega() / task.cpus}
   """
 }
 
@@ -52,6 +53,9 @@ process nanoPlot {
   tag { name }
   publishDir "${params.output_dir}/qc/nanoplot", mode: 'copy'
   cpus 4
+  memory { 8.GB * task.attempt }
+  errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'finish' }
+  maxRetries 3
 
   when:
   'nanoplot' in params.qc_tools
@@ -79,6 +83,7 @@ process nanoq {
   tag { name }
   publishDir "${params.output_dir}/qc/nanoq", mode: 'copy'
   cpus 1
+  memory 2.GB
 
   when:
   'nanoq' in params.qc_tools

subworkflows/reports.nf

@@ -47,7 +47,9 @@ process multiQC {
 process toulligQC {
   label 'toulligqc'
   publishDir "${params.output_dir}/reports/toulligqc", mode: 'copy'
-  memory 4.GB
+  memory { 8.GB * task.attempt }
+  errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'finish' }
+  maxRetries 3
 
   when:
   'toulligqc' in params.qc_tools
@@ -64,7 +66,7 @@ process toulligQC {
   script:
   if (params.experiment_name) {
     report_filename = "${slugify(params.experiment_name)}_toulligqc.html"
-    name_opt = "--report-name ${params.experiment_name}"
+    name_opt = "--report-name '${params.experiment_name}'"
   } else {
     report_filename = "toulligqc.html"
     name_opt = ''