read_format should be an input

Author: mapo9

modules/nf-core/trust4/main.nf

@@ -11,9 +11,11 @@ process TRUST4 {
     tuple val(meta), path(bam), path(reads)
     path(fasta)
     path(vdj_reference)
+    path(barcode_whitelist)
     val(cell_barcode_read)
     val(umi_read)
-    path(barcode_whitelist)
+    val(read_format)
+    
 
     output:
     tuple val(meta), path("*.tsv")                  , emit: tsv
@@ -40,7 +42,7 @@ process TRUST4 {
     def (forward, reverse) = reads.collate(2).transpose()
     def paired_end_mode = reads && (meta.single_end == false) ? "-1 ${forward[0]} -2 ${reverse[0]}" : ''
     // read format is optional
-    def readFormat = params.read_format ? "--readFormat ${params.read_format}" : ''
+    def readFormat = read_format ? "--readFormat ${read_format}" : ''
     // barcodeWhitelist is optional
     def barcodeWhitelist  = barcode_whitelist ? "--barcodeWhitelist ${barcode_whitelist}" : ""
     // add barcode information if present

modules/nf-core/trust4/meta.yml

@@ -34,15 +34,18 @@ input:
   - - vdj_reference:
         type: file
         description: reference file of V/D/J genes
+  - - barcode_whitelist:
+        type: file
+        description: BarocdeWhitelist file
   - - cell_barcode_read:
         type: string
         description: Read containing cell barcode (either R1 or R2)
   - - umi_read:
         type: string
         description: Read containing umi barcode (either R1 or R2)
-  - - barcode_whitelist:
-        type: file
-        description: BarocdeWhitelist file
+  - - read_format:
+        type: string
+        description: Specifies where in the read the barcodes and UMIs can be found.
 output:
   - tsv:
       - meta:

modules/nf-core/trust4/tests/main.nf.test

@@ -20,9 +20,11 @@ nextflow_process {
                 ])
                 input[1] = [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)] // fasta
                 input[2] = [] // ref
-                input[3] = [] // barcode
-                input[4] = [] // umi
-                input[5] = [] // barcodeWhitelist
+                input[3] = [] // barcodeWhitelist
+                input[4] = [] // barcode
+                input[5] = [] // umi
+                input[6] = [] // read format
+                
                 """
             }
         }
@@ -60,9 +62,10 @@ nextflow_process {
                 ])
                 input[1] = [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)] // fasta
                 input[2] = [] // ref
-                input[3] = [] // barcode
-                input[4] = [] // umi
-                input[5] = [] // barcodeWhitelist
+                input[3] = [] // barcodeWhitelist
+                input[4] = [] // barcode
+                input[5] = [] // umi
+                input[6] = [] // read format
                 """
             }
         }
@@ -101,9 +104,10 @@ nextflow_process {
                 ])
                 input[1] = [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)]
                 input[2] = [] // ref
-                input[3] = [] // barcode
-                input[4] = [] // umi
-                input[5] = [] // barcodeWhitelist
+                input[3] = [] // barcodeWhitelist
+                input[4] = [] // barcode
+                input[5] = [] // umi
+                input[6] = [] // read format
                 """
             }
         }