unicycler: Add parameter --long_reads

Author: sjackman

changelog.md

@@ -16,6 +16,7 @@ resolution
 - The `abyss` and `spades` components emit GFA in a secondary channel.
 - The new `bandage` component can accept either FASTA from a primary channel
   or GFA from a secondary channel.
+- The new `unicycler` component can accept long reads from a secondary channel.
 
 ### New components
 

flowcraft/generator/components/assembly.py

@@ -236,8 +236,17 @@ def __init__(self, **kwargs):
 
         self.input_type = "fastq"
         self.output_type = "fasta"
+
+        self.link_end.append({"link": "long_reads", "alias": "long_reads"})
         self.link_start.append("gfa1")
 
+        self.params = {
+            "long_reads": {
+                "default": "null",
+                "description": "FASTQ or FASTA file of long reads"
+            },
+        }
+
         self.directives = {"unicycler": {
             "cpus": 4,
             "container": "quay.io/biocontainers/unicycler",

flowcraft/generator/templates/unicycler.nf

@@ -1,3 +1,6 @@
+// True when a long_reads secondary channel is connected to this component.
+has_long_reads_{{pid}} = binding.hasVariable('long_reads_{{pid}}')
+
 process unicycler_{{pid}} {
     {% include "post.txt" ignore missing %}
 
@@ -7,6 +10,9 @@ process unicycler_{{pid}} {
 
     input:
     set sample_id, file(fastq_pair) from {{input_channel}}
+    file long_reads from has_long_reads_{{pid}} ? long_reads_{{pid}} :
+        params.long_reads{{param_id}} ? Channel.fromPath(params.long_reads{{param_id}}) :
+        Channel.value("NA")
 
     output:
     set sample_id, file('assembly.fasta') into {{output_channel}}
@@ -16,7 +22,10 @@ process unicycler_{{pid}} {
     {% endwith %}
 
     script:
-    "unicycler -t $task.cpus -o . --no_correct --no_pilon -1 ${fastq_pair[0]} -2 ${fastq_pair[1]}"
+    command = "unicycler -t $task.cpus -o . --no_correct --no_pilon -1 ${fastq_pair[0]} -2 ${fastq_pair[1]}"
+    if (params.long_reads{{param_id}})
+        command += " -l ${long_reads}"
+    command
 }
 
 {{forks}}