Add flye module

modules/flye/main.nf

@@ -20,6 +20,7 @@ process FLYE {
 
     input:
     tuple val(meta), path(reads)
+    val mode
 
     output:
     tuple val(meta), path("*.fasta"), emit: fasta
@@ -32,10 +33,9 @@ process FLYE {
 
     script:
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def mode = meta.mode
     """
     flye \\
-        --$mode \\
+        $mode \\
         $reads \\
         $options.args \\
         --threads $task.cpus \\

modules/flye/meta.yml

@@ -25,6 +25,9 @@ input:
       type: file
       description: Input file in FASTA/FASTQ format.
       pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
+  - mode:
+      type: val
+      description: flye mode ( --pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw | --nano-corr | --nano-hq )
 
 output:
   - meta:

tests/modules/flye/main.nf

@@ -5,49 +5,61 @@ nextflow.enable.dsl = 2
 include { FLYE } from '../../../modules/flye/main.nf' addParams( options: [:] )
 
 workflow test_flye_pacbio_raw {
-    input = [ [ id:'test', mode:'pacbio-raw' ], // meta map
+    input = [ [ id:'test' ], // meta map
               [ file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
             ]
 
-    FLYE ( input )
+    mode = "--pacbio-raw"
+
+    FLYE ( input, mode )
 }
 
 workflow test_flye_pacbio_corr {
-    input = [ [ id:'test', mode:'pacbio-corr' ], // meta map
+    input = [ [ id:'test' ], // meta map
               [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
             ]
 
-    FLYE ( input )
+    mode = "--pacbio-corr"
+
+    FLYE ( input, mode )
 }
 
 workflow test_flye_pacbio_hifi {
-    input = [ [ id:'test', mode:'pacbio-hifi' ], // meta map
+    input = [ [ id:'test' ], // meta map
               [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
             ]
 
-    FLYE ( input )
+    mode = "--pacbio-hifi"
+
+    FLYE ( input, mode )
 }
 
 workflow test_flye_nano_raw {
-    input = [ [ id:'test', mode:'nano-raw' ], // meta map
+    input = [ [ id:'test' ], // meta map
               [ file(params.test_data['bacteroides_fragilis']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
             ]
 
-    FLYE ( input )
+    mode = "--nano-raw"
+
+    FLYE ( input, mode )
 }
 
 workflow test_flye_nano_corr {
-    input = [ [ id:'test', mode:'nano-corr' ], // meta map
+    input = [ [ id:'test' ], // meta map
               [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
             ]
 
-    FLYE ( input )
+    mode = "--nano-corr"
+
+    FLYE ( input, mode )
 }
 
 workflow test_flye_nano_hq {
-    input = [ [ id:'test', mode:'nano-hq' ], // meta map
+    input = [ [ id:'test' ], // meta map
               [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
             ]
 
-    FLYE ( input )
+    mode = "--nano-hq"
+
+    FLYE ( input, mode )
 }