indent from review & add meta clone in the hopes it fixes Concurrentm…

…odification
nf-core · Mar 24, 2022 · 38bb8de · 38bb8de
1 parent 0858cf2
commit 38bb8de
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Showing 2 changed files with 11 additions and 7 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -227,10 +227,6 @@ process{
 process {
 
     withName: "SEQKIT_SPLIT2" {
-        //For unknown reasons occasionally 'java.util.ConcurrentModificationException' is thrown
-        //Rerunning usually works
-        //TODO not sure this works, since the error appears randomly
-        errorStrategy    = {task.exitStatus == 'java.util.ConcurrentModificationException' ? 'retry' : 'ignore'}
         ext.args         = { "--by-size ${params.split_fastq}" }
         ext.when         = { params.split_fastq > 1 }
         publishDir       = [
@@ -517,7 +513,7 @@ process{
         ]
     }
     withName: 'HAPLOTYPECALLER' {
-        ext.args         =   { params.joint_germline ? "-ERC GVCF" : "" }
+        ext.args         = { params.joint_germline ? "-ERC GVCF" : "" }
         ext.prefix       = {"${meta.id}.g"}
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') }
         publishDir       = [
@@ -643,6 +639,7 @@ process{
 
     withName: 'GATHERPILEUPSUMMARIES.*' {
         ext.prefix       = { "${meta.id}.table" }
+        ext.when         = { "${!params.no_intervals}"}
         publishDir       = [
             enabled: "${!params.no_intervals}",
             mode: params.publish_dir_mode,

diff --git a/subworkflows/local/split_fastq.nf b/subworkflows/local/split_fastq.nf
@@ -15,8 +15,15 @@ workflow SPLIT_FASTQ {
     ch_versions = Channel.empty()
 
     reads_no_split = reads_input.map{ meta, reads ->
-        meta.size = 1
-        [meta, reads]
+        [[ id:meta.id,
+            patient:meta.patient,
+            sample:meta.sample,
+            gender:meta.gender,
+            status:meta.status,
+            numLanes:meta.numLanes,
+            read_group: meta.read_group,
+            data_type:meta.data_type,
+            size:1], reads]
     }
 
     // Only if we want to split fastq files