From 8b4bfb12bb95930feafaf7b019c9cf82e2a1f0b2 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <daniel.lundin@lnu.se>
Date: Wed, 10 Nov 2021 11:27:52 +0100
Subject: [PATCH] Add log to output from bbmap/align (#1050)

---
 modules/bbmap/align/main.nf        | 4 +++-
 tests/modules/bbmap/align/test.yml | 4 ++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/bbmap/align/main.nf b/modules/bbmap/align/main.nf
index 733fd4d5..40810575 100644
--- a/modules/bbmap/align/main.nf
+++ b/modules/bbmap/align/main.nf
@@ -24,6 +24,7 @@ process BBMAP_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.log"), emit: log
     path "versions.yml"           , emit: versions
 
     script:
@@ -51,7 +52,8 @@ process BBMAP_ALIGN {
         out=${prefix}.bam \\
         $options.args \\
         threads=$task.cpus \\
-        -Xmx${task.memory.toGiga()}g
+        -Xmx${task.memory.toGiga()}g \\
+        &> ${prefix}.bbmap.log
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
diff --git a/tests/modules/bbmap/align/test.yml b/tests/modules/bbmap/align/test.yml
index 0fcc8ce9..a30713c9 100644
--- a/tests/modules/bbmap/align/test.yml
+++ b/tests/modules/bbmap/align/test.yml
@@ -6,6 +6,7 @@
   files:
     - path: output/bbmap/test.bam
       md5sum: e0ec7f1eec537acf146fac1cbdd868d1
+    - path: output/bbmap/test.bbmap.log
 
 - name: bbmap align paired end index ref
   command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c tests/config/nextflow.config
@@ -15,6 +16,7 @@
   files:
     - path: output/bbmap/test.bam
       md5sum: 345a72a0d58366d75dd263b107caa460
+    - path: output/bbmap/test.bbmap.log
 
 - name: bbmap align single end index ref
   command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c tests/config/nextflow.config
@@ -24,6 +26,7 @@
   files:
     - path: output/bbmap/test.bam
       md5sum: 95f690636581ce9b27cf8568c715ae4d
+    - path: output/bbmap/test.bbmap.log
 
 - name: bbmap align paired end index ref pigz
   command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c tests/config/nextflow.config
@@ -33,3 +36,4 @@
   files:
     - path: output/bbmap/test.bam
       md5sum: 441c4f196b9a82c7b224903538064308
+    - path: output/bbmap/test.bbmap.log