trust4 nf-core module

modules.json

@@ -34,6 +34,11 @@
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
+                    },
+                    "trust4": {
+                        "branch": "master",
+                        "git_sha": "bbb9636dbe460f45fe786d0866f8fd7337e4fc7a",
+                        "installed_by": ["modules"]
                     }
                 }
             },

modules/local/prepare_trust4_reference.nf

@@ -12,7 +12,7 @@ process PREPARE_TRUST4_REFERENCE {
     path(reference_igblast)
 
     output:
-    path("trust4_reference.fa") , emit: trust4_reference
+    tuple val(meta), path("trust4_reference.fa") , emit: trust4_reference
 
     script:
     """

subworkflows/local/fastq_input_check.nf

@@ -87,11 +87,7 @@ def create_fastq_channels(LinkedHashMap col) {
     }
     if (params.library_generation_method == "trust4") {
         meta.barcode_read = params.barcode_read
-        if (params.umi_read == "") {
-            meta.umi_read = null
-        } else {
-            meta.umi_read = params.umi_read
-        }
+        meta.umi_read = params.umi_read
         array = [ meta, [ file(col.filename_R1), file(col.filename_R2) ] ]
     } else {
         array = [ meta, [ file(col.filename_R1), file(col.filename_R2) ] ]

subworkflows/local/rnaseq_input.nf

@@ -1,5 +1,5 @@
 include { PREPARE_TRUST4_REFERENCE                                      } from '../../modules/local/prepare_trust4_reference'
-include { TRUST4                                                        } from '../../modules/local/trust4'
+include { TRUST4                                                        } from '../../modules/nf-core/trust4/main'
 include { FASTQ_INPUT_CHECK                                             } from '../../subworkflows/local/fastq_input_check'
 include { CHANGEO_CONVERTDB_FASTA as CHANGEO_CONVERTDB_FASTA_FROM_AIRR  } from '../../modules/local/changeo/changeo_convertdb_fasta'
 include { FASTP                                                         } from '../../modules/nf-core/fastp/main'
@@ -75,10 +75,18 @@ workflow RNASEQ_INPUT {
 
     PREPARE_TRUST4_REFERENCE.out.trust4_reference.dump(tag: "trust4_reference")
 
+    ch_reads_trust4.dump(tag: "trust4_input")
+
+    // create barcode and umi channels for nf-core trust4 module
+    barcode_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 ->  [meta, meta.barcode_read] }
+    umi_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 -> [meta, meta.umi_read] }
+
     TRUST4(
         ch_reads_trust4,
         PREPARE_TRUST4_REFERENCE.out.trust4_reference,
-        Channel.of([[], []]).collect()
+        Channel.of([[], []]).collect(),
+        barcode_channel,
+        umi_channel
     )
 
     ch_trust4_out = TRUST4.out.outs