Re-add piping, and hope ARFP2 doesn't pipe errors into files anymore (only reported at one cluster)

Author: jfy133

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
+- [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz
+
 ### `Dependencies`
 
 ### `Deprecated`

main.nf

@@ -811,8 +811,8 @@ process adapter_removal {
     mv *.settings output/
 
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
-    pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
+    
     """
     //PE mode, collapse and trim, outputting all reads, preserving 5p
     } else if (seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim  && !params.mergedonly && params.preserve5p) {
@@ -826,8 +826,8 @@ process adapter_removal {
     mv *.settings output/
 
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
-    pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
+
     """
     // PE mode, collapse and trim but only output collapsed reads
     } else if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) {
@@ -838,8 +838,7 @@ process adapter_removal {
     cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
         
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz >  output/${base}.pe.combined.fq
-    pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
 
     mv *.settings output/
     """
@@ -852,8 +851,7 @@ process adapter_removal {
     cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
     
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g  output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
-    pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
 
     mv *.settings output/
     """
@@ -867,8 +865,7 @@ process adapter_removal {
     cat *.collapsed.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
         
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
-    pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
 
     mv *.settings output/
     """
@@ -882,8 +879,7 @@ process adapter_removal {
     cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
     
     ## Add R_ and L_ for unmerged reads for DeDup compatibility
-    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz > output/${base}.pe.combined.fq
-    pigz -p ${task.cpus - 1} output/${base}.pe.combined.fq
+    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
 
     mv *.settings output/
     """