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

@@ -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.

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"

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"]