add dedicated output channel for trimmomatic stderr log (needed for m…

…ultiqc) (#5501)

* created new output channel capturing stderr of trimmomatic

* updated output channel for trimmomatic

* Add stub test and update snapshots

* Add stub and update tests

* Fix linting and add tee

---------

Co-authored-by: John Palmer <john.palmer@bccdc.ca>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/nf-core/trimmomatic/main.nf

@@ -12,8 +12,9 @@ process TRIMMOMATIC {
 
     output:
     tuple val(meta), path("*.paired.trim*.fastq.gz")   , emit: trimmed_reads
-    tuple val(meta), path("*.unpaired.trim_*.fastq.gz"), optional:true, emit: unpaired_reads
-    tuple val(meta), path("*.log")                     , emit: log
+    tuple val(meta), path("*.unpaired.trim_*.fastq.gz"), emit: unpaired_reads, optional:true
+    tuple val(meta), path("*_trim.log")                , emit: trim_log
+    tuple val(meta), path("*_out.log")                 , emit: out_log
     tuple val(meta), path("*.summary")                 , emit: summary
     path "versions.yml"                                , emit: versions
 
@@ -27,22 +28,46 @@ process TRIMMOMATIC {
     def output = meta.single_end ?
         "${prefix}.SE.paired.trim.fastq.gz" // HACK to avoid unpaired and paired in the trimmed_reads output
         : "${prefix}.paired.trim_1.fastq.gz ${prefix}.unpaired.trim_1.fastq.gz ${prefix}.paired.trim_2.fastq.gz ${prefix}.unpaired.trim_2.fastq.gz"
-    // TODO Give better error output
     def qual_trim = task.ext.args2 ?: ''
     """
     trimmomatic \\
         $trimmed \\
         -threads $task.cpus \\
-        -trimlog ${prefix}.log \\
+        -trimlog ${prefix}_trim.log \\
         -summary ${prefix}.summary \\
         $reads \\
         $output \\
         $qual_trim \\
-        $args
+        $args 2> >(tee ${prefix}_out.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         trimmomatic: \$(trimmomatic -version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (meta.single_end) {
+        output_command = "echo '' | gzip > ${prefix}.SE.paired.trim.fastq.gz"
+    } else {
+        output_command  = "echo '' | gzip > ${prefix}.paired.trim_1.fastq.gz"
+        output_command  = "echo '' | gzip > ${prefix}.paired.trim_2.fastq.gz"
+        output_command += "echo '' | gzip > ${prefix}.unpaired.trim_1.fastq.gz"
+        output_command += "echo '' | gzip > ${prefix}.unpaired.trim_2.fastq.gz"
+    }
+
+    """
+    $output_command
+    touch ${prefix}.summary
+    touch ${prefix}_trim.log
+    touch ${prefix}_out.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trimmomatic: \$(trimmomatic -version)
+    END_VERSIONS
+    """
+
 }

modules/nf-core/trimmomatic/meta.yml

@@ -10,7 +10,7 @@ tools:
       homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
       documentation: "https://github.com/usadellab/Trimmomatic"
       doi: "10.1093/bioinformatics/btu170"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -36,9 +36,13 @@ output:
       type: file
       description: The trimmed/modified unpaired end fastq reads
       pattern: "*.unpaired.trim_*.fastq.gz"
-  - log:
+  - trim_log:
       type: file
-      description: trimmomatic log file
+      description: trimmomatic log file, from the trim_log parameter
+      pattern: "*.log"
+  - out_log:
+      type: file
+      description: log of output from the standard out
       pattern: "*.log"
   - summary:
       type: file

modules/nf-core/trimmomatic/tests/main.nf.test

@@ -10,9 +10,6 @@ nextflow_process {
     test("Single-Read") {
         config "./nextflow_SE.config"
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -30,18 +27,19 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.trimmed_reads != null },
                 { assert process.out.trimmed_reads.get(0).get(1) ==~ ".*.SE.paired.trim.fastq.gz" },
-                { assert snapshot(process.out.versions).match("versions") },
-                { assert snapshot(process.out).match() }
+                { assert process.out.out_log.get(0).get(1) ==~ ".*.log" },
+                { assert snapshot(process.out.trimmed_reads,
+                                  process.out.trim_log,
+                                  process.out.summary,
+                                  process.out.versions
+                                  ).match() }
             )
         }
     }
 
     test("Paired-Reads") {
         config "./nextflow_PE.config"
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -61,18 +59,19 @@ nextflow_process {
                 { assert process.out.trimmed_reads != null },
                 { assert process.out.trimmed_reads.get(0).get(1).get(0) ==~ ".*.paired.trim_1.fastq.gz" },
                 { assert process.out.trimmed_reads.get(0).get(1).get(1) ==~ ".*.paired.trim_2.fastq.gz" },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") },
+                { assert process.out.out_log.get(0).get(1) ==~ ".*.log" },
+                { assert snapshot(process.out.trimmed_reads,
+                                  process.out.trim_log,
+                                  process.out.summary,
+                                  process.out.versions
+                                  ).match() }
             )
         }
     }
 
     test("No Adaptors") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -92,4 +91,28 @@ nextflow_process {
             )
         }
     }
+
+    test("Single-Read - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }