Merge pull request #149 from natir/bcalm

Add bcalm to flowcraft

Author: ODiogoSilva

changelog.md

@@ -23,6 +23,7 @@ resolution
 - Added component `bandage`.
 - Added component `unicycler`.
 - Added component `prokka`.
+- Added component `bcalm`.
 
 ### Minor/Other changes
 

flowcraft/generator/components/assembly.py

@@ -4,6 +4,48 @@
 except ImportError:
     from flowcraft.generator.process import Process
 
+class Bcalm(Process):
+    """Bcalm 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.params = {
+            "bcalmKmerSize": {
+                "default": 31,
+                "description":
+                    "size of a kmer"
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
+	    }
+        }
+
+        self.directives = {"bcalm": {
+            "cpus": 4,
+            "memory": "{ 5.GB * task.attempt }",
+            "container": "quay.io/biocontainers/bcalm",
+            "version": "2.2.0--hd28b015_2",
+            "scratch": "true"
+        }}
+
 
 class Spades(Process):
     """Spades process template interface

flowcraft/generator/engine.py

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

flowcraft/generator/templates/bcalm.nf

@@ -0,0 +1,38 @@
+// Check parameter
+if ( !params.bcalmKmerSize{{ param_id }}.toString().isNumber() ){
+    exit 1, "'bcalmKmerSize{{ param_id }}' parameter must be a number. Provided value: '${params.bcalmKmes%rSize{{ param_id }}}'"
+}
+
+// Clear
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
+
+process bcalm_{{ pid }} {
+    {% include "post.txt" ignore missing %}
+
+    tag { sample_id }
+    publishDir "reports/assembly/quast_{{pid}}/$sample_id"
+
+    input:
+    set sample_id, file(fastq) from {{input_channel}}
+    val KmerSize from Channel.value(params.bcalmKmerSize{{param_id}})
+    
+output:
+    file "*.unitig.fa"
+    {% with task_name="bcalm" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    script:
+    """
+    {
+	bcalm -in $fastq -out unitig -kmer-size $KmerSize"
+
+  	if [ "$clear" = "true" ];
+	then
+    	    find . -type f  -print | egrep "work/.*(h5)|(glue)" | xargs -L 1 rm
+	fi
+    }
+    """
+}
+