unicycler: Add parameter --long_fastq

assemblerflow · Oct 22, 2018 · e3fb197 · e3fb197
1 parent 97b50cd
commit e3fb197
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/flowcraft/generator/templates/unicycler.nf b/flowcraft/generator/templates/unicycler.nf
@@ -7,6 +7,9 @@ process unicycler_{{pid}} {
 
     input:
     set sample_id, file(fastq_pair) from {{input_channel}}
+    file long_fastq from params.long_fastq{{param_id}} ?
+        Channel.fromPath(params.long_fastq{{param_id}}) :
+        Channel.value("NA")
 
     output:
     set sample_id, file('assembly.fasta') into {{output_channel}}
@@ -16,7 +19,10 @@ 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_fastq{{param_id}})
+        command += " -l ${long_fastq}"
+    command
 }
 
 {{forks}}