Fix fastp merge issue with subworkflow (#7237)

* Fix fastp merge issue with subworkflow

* Restore file

* Update subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml

* Apply suggestions from code review

subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf

@@ -111,6 +111,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
     stranded_threshold   // float: The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5
     unstranded_threshold // float: The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'
     skip_linting         // boolean: true/false
+    fastp_merge          // boolean: true/false: whether to stitch paired end reads together in FASTP output
 
     main:
 
@@ -191,7 +192,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
             skip_trimming,
             [],
             save_trimmed,
-            save_trimmed,
+            fastp_merge,
             min_trimmed_reads
         )
         ch_filtered_reads      = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads

subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml

@@ -142,6 +142,10 @@ input:
   - skip_linting:
       type: boolean
       description: Whether to skip linting of FastQ files
+  - fastp_merge:
+      type: boolean
+      description: |
+        For FASTP, save merged fastqs stitching together read1 and read2 for paired end reads
 
 output:
   - reads:

subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test

@@ -56,6 +56,7 @@ nextflow_workflow {
                 input[20] = 0.8            // stranded_threshold
                 input[21] = 0.1            // unstranded_threshold
                 input[22] = false          // skip_linting
+                input[23] = true           // fastp_merge
                 """
             }
         }
@@ -121,6 +122,7 @@ nextflow_workflow {
                 input[20] = 0.8            // stranded_threshold
                 input[21] = 0.1            // unstranded_threshold
                 input[22] = false          // skip_linting
+                input[23] = true           // fastp_merge
                 """
             }
         }