Update filtlong module to output log file (#1873)

Redirect logging information to log file in filtlong module

modules/filtlong/main.nf

@@ -12,7 +12,8 @@ process FILTLONG {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
-    path "versions.yml"                                     , emit: versions
+    tuple val(meta), path("*.log")     , emit: log
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,6 +28,7 @@ process FILTLONG {
         $short_reads \\
         $args \\
         $longreads \\
+        2> ${prefix}.log \\
         | gzip -n > ${prefix}.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml

modules/filtlong/meta.yml

@@ -45,6 +45,11 @@ output:
       type: file
       description: Filtered (compressed) fastq file
       pattern: "*.fastq.gz"
+  - log:
+      type: file
+      description: Standard error logging file containing summary statistics
+      pattern: "*.log"
 
 authors:
   - "@d4straub"
+  - "@sofstam"

tests/modules/filtlong/test.yml

@@ -4,8 +4,8 @@
     - filtlong
   files:
     - path: output/filtlong/test_lr.fastq.gz
-      contains:
-        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
+    - path: output/filtlong/test_lr.log
+      contains: ["Scoring long reads"]
 
 - name: filtlong test_filtlong_illumina_se
   command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
@@ -13,8 +13,8 @@
     - filtlong
   files:
     - path: output/filtlong/test_lr.fastq.gz
-      contains:
-        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
+    - path: output/filtlong/test_lr.log
+      contains: ["Scoring long reads"]
 
 - name: filtlong test_filtlong_illumina_pe
   command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
@@ -22,5 +22,5 @@
     - filtlong
   files:
     - path: output/filtlong/test_lr.fastq.gz
-      contains:
-        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
+    - path: output/filtlong/test_lr.log
+      contains: ["Scoring long reads"]