Update PORECHOP module to output log file (#1870)

Update porechop to output log file

modules/porechop/main.nf

@@ -12,6 +12,7 @@ process PORECHOP {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.log")     , emit: log
     path "versions.yml"                , emit: versions
 
     when:
@@ -25,7 +26,8 @@ process PORECHOP {
         -i $reads \\
         -t $task.cpus \\
         $args \\
-        -o ${prefix}.fastq.gz
+        -o ${prefix}.fastq.gz \\
+        > ${prefix}.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/porechop/meta.yml

@@ -38,6 +38,10 @@ output:
       type: file
       description: Demultiplexed and/or adapter-trimmed fastq.gz file
       pattern: "*.{fastq.gz}"
+  - log:
+      type: file
+      description: Log file containing stdout information
+      pattern: "*.log"
 
 authors:
   - "@ggabernet"
@@ -48,3 +52,4 @@ authors:
   - "@jonasscheid"
   - "@jonoave"
   - "@GokceOGUZ"
+  - "@jfy133"

tests/modules/porechop/test.yml

@@ -1,7 +1,9 @@
 - name: porechop test_porechop
-  command: nextflow run ./tests/modules/porechop -entry test_porechop -c ./tests/config/nextflow.config -c ./tests/modules/porechop/nextflow.config
+  command: nextflow run ./tests/modules/porechop -entry test_porechop -c ./tests/config/nextflow.config  -c ./tests/modules/porechop/nextflow.config
   tags:
     - porechop
   files:
     - path: output/porechop/test_porechop.fastq.gz
       md5sum: 08f314ae9f162c8dcc27e5b513d2064d
+    - path: output/porechop/test_porechop.log
+      contains: ["Saving trimmed reads to file"]