From b6ed584443ad68ac41e6975994139454a4f23c18 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 13 Jul 2022 11:26:27 +0200
Subject: [PATCH] Update MOTUS/PROFILE  module to output log file (#1871)

* Add saving of stderr output as a log file as it contains summary statistics

* Apply suggestions from code review
---
 modules/motus/profile/main.nf        | 4 +++-
 modules/motus/profile/meta.yml       | 4 ++++
 tests/modules/motus/profile/test.yml | 2 ++
 3 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/modules/motus/profile/main.nf b/modules/motus/profile/main.nf
index 27479844..bd7a1273 100644
--- a/modules/motus/profile/main.nf
+++ b/modules/motus/profile/main.nf
@@ -15,6 +15,7 @@ process MOTUS_PROFILE {
     tuple val(meta), path("*.out"), emit: out
     tuple val(meta), path("*.bam"), optional: true, emit: bam
     tuple val(meta), path("*.mgc"), optional: true, emit: mgc
+    tuple val(meta), path("*.log")                , emit: log
     path "versions.yml"           , emit: versions
 
     when:
@@ -36,7 +37,8 @@ process MOTUS_PROFILE {
         $refdb \\
         -t $task.cpus \\
         -n $prefix \\
-        -o ${prefix}.out
+        -o ${prefix}.out \\
+        2> ${prefix}.log
 
     ## mOTUs version number is not available from command line.
     ## mOTUs save the version number in index database folder.
diff --git a/modules/motus/profile/meta.yml b/modules/motus/profile/meta.yml
index 19803bdc..3c3b6604 100644
--- a/modules/motus/profile/meta.yml
+++ b/modules/motus/profile/meta.yml
@@ -56,6 +56,10 @@ output:
       type: file
       description: Optional intermediate mgc read count table file saved with `-M`.
       pattern: "*.{mgc}"
+  - log:
+      type: file
+      description: Standard error logging file containing summary statistics
+      pattern: "*.log"
 
 authors:
   - "@jianhong"
diff --git a/tests/modules/motus/profile/test.yml b/tests/modules/motus/profile/test.yml
index 8031d5ab..f5ce5bf7 100644
--- a/tests/modules/motus/profile/test.yml
+++ b/tests/modules/motus/profile/test.yml
@@ -6,3 +6,5 @@
   files:
     - path: output/motus/test.out
       contains: ["#consensus_taxonomy\ttest"]
+    - path: output/motus/test.log
+      contains: ["Finished computation"]