Merge pull request #156 from sjackman/unicycler

Add unicycler

Author: ODiogoSilva

changelog.md

@@ -17,6 +17,8 @@ resolution
 ### New components
 
 - Added component `abyss`.
+- Added component `bandage`.
+- Added component `unicycler`.
 
 ### Minor/Other changes
 

flowcraft/generator/components/assembly.py

@@ -216,3 +216,29 @@ def __init__(self, **kwargs):
             "version": "2.1.1",
             "scratch": "true"
         }}
+
+class Unicycler(Process):
+    """Unicycler process template interface
+
+    This process is set with:
+
+        - ``input_type``: fastq
+        - ``output_type``: assembly
+        - ``ptype``: assembly
+
+    """
+
+    def __init__(self, **kwargs):
+
+        super().__init__(**kwargs)
+
+        self.input_type = "fastq"
+        self.output_type = "fasta"
+        self.link_start.append("gfa1")
+
+        self.directives = {"unicycler": {
+            "cpus": 4,
+            "container": "quay.io/biocontainers/unicycler",
+            "version": "0.4.7--py36hdbcaa40_0",
+            "scratch": "true"
+        }}

flowcraft/generator/engine.py

@@ -104,6 +104,7 @@
         "split_assembly": meta.SplitAssembly,
         "trimmomatic": readsqc.Trimmomatic,
         "true_coverage": readsqc.TrueCoverage,
+        "unicycler": assembly.Unicycler,
         "viral_assembly": assembly.ViralAssembly,
 }
 

flowcraft/generator/templates/unicycler.nf

@@ -0,0 +1,22 @@
+process unicycler_{{pid}} {
+    {% include "post.txt" ignore missing %}
+
+    tag { sample_id }
+    publishDir 'results/assembly/unicycler_{{pid}}/', pattern: 'assembly.fasta'
+    publishDir 'results/assembly/unicycler_{{pid}}/', pattern: 'assembly.gfa'
+
+    input:
+    set sample_id, file(fastq_pair) from {{input_channel}}
+
+    output:
+    set sample_id, file('assembly.fasta') into {{output_channel}}
+    file "assembly.gfa" into gfa1_{{pid}}
+    {% with task_name="unicycler" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    script:
+    "unicycler -t $task.cpus -o . --no_correct --no_pilon -1 ${fastq_pair[0]} -2 ${fastq_pair[1]}"
+}
+
+{{forks}}