Replaced param with input val channel (#595)

* Replaced param with input val channel

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review (missed one)

* YAML lint

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/fastp/main.nf

@@ -20,6 +20,7 @@ process FASTP {
 
     input:
     tuple val(meta), path(reads)
+    val   save_trimmed_fail
 
     output:
     tuple val(meta), path('*.trim.fastq.gz'), emit: reads
@@ -34,7 +35,7 @@ process FASTP {
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     if (meta.single_end) {
-        def fail_fastq = params.save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
+        def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         fastp \\
@@ -49,7 +50,7 @@ process FASTP {
         echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
         """
     } else {
-        def fail_fastq = params.save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+        def fail_fastq = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
         """
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz

tests/modules/fastp/main.nf

@@ -11,8 +11,9 @@ workflow test_fastp_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
+    save_trimmed_fail = false
 
-    FASTP ( input )
+    FASTP ( input, save_trimmed_fail )
 }
 
 //
@@ -23,7 +24,32 @@ workflow test_fastp_paired_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
+    save_trimmed_fail = false
 
-    FASTP ( input )
+    FASTP ( input, save_trimmed_fail )
 }
 
+//
+// Test with single-end data with saving trimming fails
+//
+workflow test_fastp_single_end_trim_fail {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = true
+
+    FASTP ( input, save_trimmed_fail )
+}
+
+//
+// Test with paired-end data with saving trimming fails
+//
+workflow test_fastp_paired_end_trim_fail {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    save_trimmed_fail = true
+
+    FASTP ( input, save_trimmed_fail )
+}

tests/modules/fastp/test.yml

@@ -36,3 +36,48 @@
       md5sum: e2257263668dc8a75d95475099fb472d
     - path: output/fastp/test_2.trim.fastq.gz
       md5sum: 9eff7203596580cc5e42aceab4a469df
+
+- name: fastp test_fastp_single_end_trim_fail
+  command: nextflow run tests/modules/fastp -entry test_fastp_single_end_trim_fail -c tests/config/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
+        - "single end (151 cycles)"
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "Q20 bases: 12922(92.9841%)"
+        - "reads passed filter: 99"
+    - path: output/fastp/test.trim.fastq.gz
+      md5sum: e2257263668dc8a75d95475099fb472d
+    - path: output/fastp/test.fastp.json
+      md5sum: ee65a46d6e59fa556f112727b8a902ce
+    - path: output/fastp/test.fail.fastq.gz
+      md5sum: de315d397c994d8e66bafc7a8dc11070
+
+- name: fastp test_fastp_paired_end_trim_fail
+  command: nextflow run tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c tests/config/nextflow.config
+  tags:
+    - fastp
+  files:
+    - path: output/fastp/test.fastp.html
+      contains:
+        - "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
+        - "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
+    - path: output/fastp/test.fastp.log
+      contains:
+        - "No adapter detected for read1"
+        - "Q30 bases: 12281(88.3716%)"
+    - path: output/fastp/test.fastp.json
+      contains:
+        - '"passed_filter_reads": 198'
+    - path: output/fastp/test_1.trim.fastq.gz
+      md5sum: e2257263668dc8a75d95475099fb472d
+    - path: output/fastp/test_2.trim.fastq.gz
+      md5sum: 9eff7203596580cc5e42aceab4a469df
+    - path: output/fastp/test_1.fail.fastq.gz
+      md5sum: e62ff0123a74adfc6903d59a449cbdb0
+    - path: output/fastp/test_2.fail.fastq.gz
+      md5sum: f52309b35a7c15cbd56a9c3906ef98a5