Merge pull request #139 from assemblerflow/assembly_graph

Assembly graph results

Author: ODiogoSilva

flowcraft/generator/components/metagenomics.py

@@ -139,6 +139,12 @@ def __init__(self, **kwargs):
                     "'default', megahit will use the default k-mer lengths. "
                     "(default: $params.megahitKmers)"
             },
+            "fastg": {
+                "default": "false",
+                "description":
+                    "Converts megahit intermediate contigs to fastg"
+
+            },
             "clearInput": {
                 "default": "false",
                 "description":
@@ -155,7 +161,17 @@ def __init__(self, **kwargs):
             "container": "flowcraft/megahit",
             "version": "1.1.3-0.1",
             "scratch": "true"
-        }}
+        },
+            "megahit_fastg": {
+                "container": "flowcraft/megahit",
+                "version": "1.1.3-0.1",
+            }
+        }
+
+        self.status_channels = [
+            "megahit",
+            "megahit_fastg"
+        ]
 
 
 class Metaspades(Process):

flowcraft/generator/templates/megahit.nf

@@ -23,6 +23,7 @@ process megahit_{{ pid }} {
 
     output:
     set sample_id, file('*megahit*.fasta') into {{ output_channel }}
+    set sample_id, file('megahit/intermediate_contigs/k*.contigs.fa') into IN_fastg{{ pid }}
     {% with task_name="megahit" %}
     {%- include "compiler_channels.txt" ignore missing -%}
     {% endwith %}
@@ -31,8 +32,38 @@ process megahit_{{ pid }} {
     template "megahit.py"
 
 }
+IN_fastg = Channel.create()
 
-{{ forks }}
+fastg = params.fastg{{ param_id }} ? "true" : "false"
+if (fastg) {
+    process megahit_fastg_{{ pid }}{
 
+        // Send POST request to platform
+        {% include "post.txt" ignore missing %}
 
+        tag { sample_id }
+        publishDir "results/assembly/megahit_{{ pid }}/$sample_id", pattern: "*.fastg"
 
+        input:
+        set sample_id, file(kmer_files) from IN_fastg{{ pid }}
+
+        output:
+        file "*.fastg"
+        {% with task_name="megahit_fastg" %}
+        {%- include "compiler_channels.txt" ignore missing -%}
+        {% endwith %}
+
+        script:
+        """
+        for kmer_file in ${kmer_files};
+        do
+            echo \$kmer_file
+            k=\$(echo \$kmer_file | cut -d '.' -f 1);
+            echo \$k
+            megahit_toolkit contig2fastg \$k \$kmer_file > \$kmer_file'.fastg';
+        done
+        """
+    }
+}
+
+{{ forks }}

flowcraft/generator/templates/spades.nf

@@ -24,6 +24,8 @@ process spades_{{ pid }} {
 
     tag { sample_id }
     publishDir 'results/assembly/spades_{{ pid }}/', pattern: '*_spades*.fasta', mode: 'copy'
+    publishDir "reports/assembly/spades_{{ pid }}/$sample_id", pattern: "*.gfa", mode: "copy"
+    publishDir "reports/assembly/spades_{{ pid }}/$sample_id", pattern: "*.fastg", mode: "copy"
 
     input:
     set sample_id, file(fastq_pair), max_len from {{ input_channel }}.join(SIDE_max_len_{{ pid }})
@@ -33,6 +35,8 @@ process spades_{{ pid }} {
 
     output:
     set sample_id, file('*_spades*.fasta') into {{ output_channel }}
+    file "*.fastg"
+    file "*.gfa"
     {% with task_name="spades" %}
     {%- include "compiler_channels.txt" ignore missing -%}
     {% endwith %}