Add long read preprocessing subworkflow

subworkflows/local/longread_preprocessing.nf

@@ -0,0 +1,34 @@
+
+include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
+include { PORECHOP              } from '../../modules/nf-core/modules/porechop/main'
+
+workflow LONGREAD_PREPROCESSING {
+    take:
+    reads
+
+    main:
+    ch_versions      = Channel.empty()
+    ch_multiqc_files = Channel.empty()
+
+    PORECHOP ( reads )
+
+    ch_processed_reads = PORECHOP.out.reads
+                                .dump(tag: "pre_fastqc_check")
+                                .map {
+                                        meta, reads ->
+                                        def meta_new = meta.clone()
+                                        meta_new['single_end'] = 1
+                                        [ meta_new, reads ]
+                                    }
+
+    FASTQC_POST ( PORECHOP.out.reads )
+    ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} )
+
+
+    emit:
+    reads    = ch_processed_reads   // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions          // channel: [ versions.yml ]
+    mqc      = ch_multiqc_files
+}
+