From c341b3783e78831b7bfa276dd582b949d3631656 Mon Sep 17 00:00:00 2001
From: Shaun Jackman <sjackman@gmail.com>
Date: Mon, 22 Oct 2018 16:36:22 -0700
Subject: [PATCH] Add porechop

---
 changelog.md                                  |  1 +
 .../components/reads_quality_control.py       | 34 +++++++++++++++++++
 flowcraft/generator/engine.py                 |  1 +
 flowcraft/generator/templates/porechop.nf     | 28 +++++++++++++++
 4 files changed, 64 insertions(+)
 create mode 100644 flowcraft/generator/templates/porechop.nf

diff --git a/changelog.md b/changelog.md
index 41ef21ae..00979308 100644
--- a/changelog.md
+++ b/changelog.md
@@ -22,6 +22,7 @@ resolution
 
 - Added component `abyss`.
 - Added component `bandage`.
+- Added component `porechop`.
 - Added component `unicycler`.
 
 ### Minor/Other changes
diff --git a/flowcraft/generator/components/reads_quality_control.py b/flowcraft/generator/components/reads_quality_control.py
index de0426c4..04b1aecd 100644
--- a/flowcraft/generator/components/reads_quality_control.py
+++ b/flowcraft/generator/components/reads_quality_control.py
@@ -433,3 +433,37 @@ def __init__(self, **kwargs):
         self.status_channels = [
             "downsample_fastq"
         ]
+
+class Porechop(Process):
+    """Porechop trims adapters from Oxford Nanopore reads.
+
+    This process is set with:
+
+        - ``input_type``: fastq
+        - ``output_type``: fastq
+        - ``ptype``: pre_assembly
+    """
+
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+
+        self.input_type = "fastq"
+        self.output_type = "fastq"
+
+        self.link_end.append({"link": "raw_long_reads", "alias": "raw_long_reads"})
+        self.link_start.append("long_reads")
+
+        self.params = {
+            "long_reads": {
+                "default": "null",
+                "description": "FASTQ or FASTA file of long reads"
+            },
+        }
+
+        self.directives = {
+            "porechop": {
+                "cpus": 4,
+                "container": "quay.io/biocontainers/porechop",
+                "version": "0.2.3_seqan2.1.1--py36h2d50403_3"
+            }
+        }
diff --git a/flowcraft/generator/engine.py b/flowcraft/generator/engine.py
index 4f509d38..4edc3ede 100644
--- a/flowcraft/generator/engine.py
+++ b/flowcraft/generator/engine.py
@@ -88,6 +88,7 @@
         "momps": typing.Momps,
         "patho_typing": typing.PathoTyping,
         "pilon": ap.Pilon,
+        "porechop": readsqc.Porechop,
         "process_skesa": ap.ProcessSkesa,
         "process_spades": ap.ProcessSpades,
         "progressive_mauve":alignment.ProgressiveMauve,
diff --git a/flowcraft/generator/templates/porechop.nf b/flowcraft/generator/templates/porechop.nf
new file mode 100644
index 00000000..99f3507c
--- /dev/null
+++ b/flowcraft/generator/templates/porechop.nf
@@ -0,0 +1,28 @@
+// True when a raw_long_reads secondary channel is connected to this component.
+has_raw_long_reads_{{pid}} = binding.hasVariable('raw_long_reads_{{pid}}')
+
+process porechop_{{pid}} {
+    {% include "post.txt" ignore missing %}
+
+    publishDir "results/porechop_{{pid}}", pattern: "*.fastq.gz"
+    publishDir "reports/porechop_{{pid}}", pattern: "*.log"
+
+    tag { sample_id }
+
+    input:
+    set sample_id, file(fastq_pair) from {{input_channel}}
+    file raw_long_reads from has_raw_long_reads_{{pid}} ? raw_long_reads_{{pid}} :
+        Channel.fromPath(params.long_reads{{param_id}})
+
+    output:
+    set sample_id, file(fastq_pair) into {{output_channel}}
+    file "${sample_id}.fastq.gz" into long_reads_{{pid}}
+    {% with task_name="porechop" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    script:
+    "time porechop -t $task.cpus --format fastq.gz -i ${raw_long_reads} -o ${sample_id}.fastq.gz >${sample_id}.log"
+}
+
+{{ forks }}