From f6b07b1711a313f78e1b11d71175370bc0643872 Mon Sep 17 00:00:00 2001
From: Matt Parker <matt.parker@nanoporetech.com>
Date: Thu, 9 Jun 2022 13:43:53 +0000
Subject: [PATCH] Restrict assembly to only reads from mpx

---
 CHANGELOG.md         | 3 ++-
 main.nf              | 9 +++++----
 nextflow.config      | 2 +-
 nextflow_schema.json | 2 +-
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 19d8018..a764161 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,9 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+## [v0.0.2]
 ### Changed
 - Tidied up docs
+- Restricting assembly to only reads that map to mpx
 
 ## [v0.0.1]
 
diff --git a/main.nf b/main.nf
index aa36b08..03eda6c 100644
--- a/main.nf
+++ b/main.nf
@@ -110,17 +110,18 @@ process flyeAssembly {
     label "wfmpx"
     cpus params.threads
     input:
-        tuple val(sample_id), val(type), path(sample_fastq), path(sample_stats)
+        tuple val(sample_id), val(type), path("${sample_id}.bam"), path("${sample_id}.bam.bai")
         path reference
     output:
         tuple val(sample_id), val(type), path("medaka/consensus.fasta"), path("${sample_id}_assembly_mapped.bam"), path("${sample_id}_assembly.bed")
     script:
     """
-    flye --nano-raw ${sample_fastq}  -g 197k -t ${params.threads} --meta -o flye
+    samtools bam2fq ${sample_id}.bam > ${sample_id}_restricted.fastq
+    flye --nano-raw ${sample_id}_restricted.fastq  -g 197k -t ${params.threads} --meta -o flye
 
     # polish assembly with medaka
 
-    medaka_consensus -i ${sample_fastq} -t ${params.threads} -d flye/assembly.fasta ${params.medaka_options}
+    medaka_consensus -i ${sample_id}_restricted.fastq -t ${params.threads} -d flye/assembly.fasta ${params.medaka_options}
 
     minimap2 -ax map-ont ${reference} medaka/consensus.fasta | samtools view -bh - | samtools sort - > ${sample_id}_assembly_mapped.bam
 
@@ -221,7 +222,7 @@ workflow pipeline {
         workflow_params = getParams()
 
         if (params.assembly == true) {
-          assembly = flyeAssembly(summary.sample, reference)
+          assembly = flyeAssembly(alignment.alignment, reference)
         }
 
 
diff --git a/nextflow.config b/nextflow.config
index 3c20614..3ca81c5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -17,7 +17,7 @@ params {
     sample = null
     sample_sheet = null
     sanitize_fastq = false
-    wfversion = "v0.0.1"
+    wfversion = "v0.0.2"
     threads = 4
     assembly = true
     medaka_options = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a0a045a..6fa230c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -127,7 +127,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.0.1",
+            "default": "v0.0.2",
             "hidden": true
         },
         "monochrome_logs": {