Fix FASTQ concatenation

Author: nictru

subworkflows/local/bsj_detection.nf

@@ -228,7 +228,6 @@ workflow BSJ_DETECTION {
         .mix( ch_bsj_bed_combined.map{ meta, f -> true } )
         // If no circular RNAs were found, stop the pipeline
         .filter{ it }
-        .view()
         .ifEmpty{
             error (
                 "No circular RNAs were found by at least ${params.min_tools} tools and in at least ${params.min_samples} samples.\n" +

subworkflows/local/utils_nfcore_circrna_pipeline/main.nf

@@ -86,10 +86,6 @@ workflow PIPELINE_INITIALISATION {
         .map { samplesheet ->
             validateInputSamplesheet(samplesheet)
         }
-        .map {
-            meta, fastqs ->
-                return [ meta, fastqs.flatten() ]
-        }
         .set { ch_samplesheet }
 
     emit:

workflows/circrna/main.nf

@@ -75,17 +75,19 @@ workflow CIRCRNA {
         .branch {
             meta, fastqs ->
                 single  : fastqs.size() == 1
-                    return [ meta, fastqs ]
+                    return [ meta, fastqs.flatten() ]
                 multiple: fastqs.size() > 1
-                    return [ meta, fastqs ]
+                    return [ meta, fastqs.flatten() ]
         }
         .set { ch_fastq }
 
     // MODULE:
     // Concatenate FastQ files from same sample if required
     CAT_FASTQ (ch_fastq.multiple)
         .reads
-        .mix(ch_fastq.single)
+        .mix(
+            ch_fastq.single
+        )
         .set { ch_cat_fastq }
     ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)