From 9481c8403198889911cf647287c25ed11b28f4fa Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 10 Mar 2022 15:16:52 +0100
Subject: [PATCH] Re-add piping, and hope ARFP2 doesn't pipe errors into files
 anymore (only reported at one cluster)

---
 CHANGELOG.md |  2 ++
 main.nf      | 20 ++++++++------------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a0b308b4c..665a78695 100644
--- a/CHANGELOG.md
+++ b/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`
diff --git a/main.nf b/main.nf
index 6f89cd0fa..85c5bc76b 100644
--- a/main.nf
+++ b/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/
     """