From 50e209ba7daabd63abb401e562c4a1ad6c36b763 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 9 Sep 2021 18:57:07 +0200
Subject: [PATCH] Separate Adapterremovalfixprefix and pigz

---
 CHANGELOG.md |  1 +
 main.nf      | 18 ++++++++++++------
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c7ed9289..35dd68c00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#787](https://github.com/nf-core/eager/issues/787) Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander)
 - Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
 - [#790](https://github.com/nf-core/eager/issues/790) Fixed kraken2 report file-name collision when sample names have `.` in them
+- [#792](https://github.com/nf-core/eager/issues/792) Fixed java error messages for AdapterRemovalFixPrefix being hidden in output
 
 ### `Dependencies`
 
diff --git a/main.nf b/main.nf
index a3a42a489..b76f3da16 100644
--- a/main.nf
+++ b/main.nf
@@ -811,7 +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 | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
+    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
     """
     //PE mode, collapse and trim, outputting all reads, preserving 5p
     } else if (seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim  && !params.mergedonly && params.preserve5p) {
@@ -825,7 +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 | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz
+    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
     """
     // PE mode, collapse and trim but only output collapsed reads
     } else if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) {
@@ -836,7 +838,8 @@ 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 | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz
+    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
 
     mv *.settings output/
     """
@@ -849,7 +852,8 @@ 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 | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
+    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
 
     mv *.settings output/
     """
@@ -863,7 +867,8 @@ 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 | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz
+    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
 
     mv *.settings output/
     """
@@ -877,7 +882,8 @@ 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 | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz
+    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
 
     mv *.settings output/
     """