Merge pull request #150 from sjackman/bandage

Add bandage

Author: ODiogoSilva

flowcraft/generator/components/assembly_processing.py

@@ -230,6 +230,37 @@ def __init__(self, **kwargs):
             }
         }
 
+class Bandage(Process):
+    """Visualize the assembly using Bandage
+
+    This process is set with:
+
+        - ``input_type``: assembly
+        - ``output_type``: none
+        - ``ptype``: post_assembly
+
+    """
+
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+
+        self.input_type = "fasta"
+        self.output_type = None
+
+        self.params = {
+            "reference": {
+                "default": "null",
+                "description": "Align the assembly to this reference genome using BLAST"
+            },
+        }
+
+        self.directives = {
+            "bandage": {
+                "container": "flowcraft/bandage",
+                "version": "0.8.1"
+            }
+        }
+
 class Quast(Process):
     """Assess assembly quality using QUAST
 

flowcraft/generator/engine.py

@@ -58,6 +58,7 @@
         "abyss": assembly.Abyss,
         "abricate": annotation.Abricate,
         "assembly_mapping": ap.AssemblyMapping,
+        "bandage": ap.Bandage,
         "bowtie": mapping.Bowtie,
         "card_rgi": annotation.CardRgi,
         "check_coverage": readsqc.CheckCoverage,

flowcraft/generator/templates/bandage.nf

@@ -0,0 +1,48 @@
+if (params.reference{{param_id}} != null) {
+    process bandage_{{pid}} {
+        {% include "post.txt" ignore missing %}
+
+        tag { sample_id }
+        publishDir "reports/assembly/bandage_{{pid}}/$sample_id"
+
+        input:
+        set sample_id, file(assembly) from {{input_channel}}
+        file reference from Channel.fromPath(params.reference{{param_id}})
+
+        output:
+        file "*.png *.svg"
+        {% with task_name="bandage" %}
+        {%- include "compiler_channels.txt" ignore missing -%}
+        {% endwith %}
+
+        script:
+        """
+        time Bandage image $assembly ${assembly}.png >>.command.log 2>&1
+        time Bandage image $assembly ${assembly}.svg >>.command.log 2>&1
+        time Bandage image $assembly ${assembly}.ref.png --query $reference >>.command.log 2>&1
+        time Bandage image $assembly ${assembly}.ref.svg --query $reference >>.command.log 2>&1
+        """
+    }
+} else {
+    process bandage_{{pid}} {
+        {% include "post.txt" ignore missing %}
+
+        tag { sample_id }
+        publishDir "reports/assembly/bandage_{{pid}}/$sample_id"
+
+        input:
+        set sample_id, file(assembly) from {{input_channel}}
+
+        output:
+        file "*.png *.svg"
+        {% with task_name="bandage" %}
+        {%- include "compiler_channels.txt" ignore missing -%}
+        {% endwith %}
+
+        script:
+        """
+        time Bandage image $assembly ${assembly}.png >>.command.log 2>&1
+        time Bandage image $assembly ${assembly}.svg >>.command.log 2>&1
+        """
+    }
+}