From a57488007751868ee149c2fe1d66081abb22bb08 Mon Sep 17 00:00:00 2001
From: Biowilko <sam1.wilkinson1@gmail.com>
Date: Tue, 3 Sep 2024 18:22:44 +0100
Subject: [PATCH] Enable depth normalisation and fix bcftools bug

---
 modules/illumina.nf       |  6 +++---
 nextflow.config           |  2 +-
 nextflow_schema.json      |  6 ++++++
 workflows/illuminaMpxv.nf | 12 ++++++------
 4 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/modules/illumina.nf b/modules/illumina.nf
index 2bf4faa..ba702a3 100644
--- a/modules/illumina.nf
+++ b/modules/illumina.nf
@@ -29,9 +29,9 @@ process normalizeDepth {
 
     label  'process_low'
 
-    container 'community.wave.seqera.io/library/bbmap:39.06--5b971f29ed092959'
+    container 'docker.io/bryce911/bbtools:39.08'
 
-    conda 'bioconda::bbmap=39.06'
+    conda 'bioconda::bbmap=39.08'
 
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: '*_norm_R{1,2}.fq.gz', mode: 'copy'
 
@@ -270,7 +270,7 @@ process callConsensusFreebayes {
     CTG_NAME=\$(head -n1 ${ref} | sed 's/>//')
 
     # apply remaninng variants, including indels
-    bcftools consensus -f ${sampleName}.ambiguous.fa -m ${sampleName}.mask.txt ${sampleName}.fixed.norm.vcf.gz | sed s/\$CTG_NAME/${sampleName}/ > ${sampleName}.consensus.fa
+    bcftools consensus -s - -f ${sampleName}.ambiguous.fa -m ${sampleName}.mask.txt ${sampleName}.fixed.norm.vcf.gz | sed s/\$CTG_NAME/${sampleName}/ > ${sampleName}.consensus.fa
     """
 }
 
diff --git a/nextflow.config b/nextflow.config
index 5a9046e..d1a9373 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
   description = 'Epi2me compatible Nextflow pipeline for processing ARTIC tiling amplicon Illumina sequencing reads from monkeypox virus (MPXV) samples.'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '1.0.11'
+  version = '1.0.12'
 }
 
 // Load base.config by default for all pipelines
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 97ca62c..4aaa5ee 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -124,6 +124,12 @@
           "title": "Variant caller minimum depth",
           "default": 10,
           "description": "Minimum coverage depth to call variant"
+        },
+        "skip_normalize_depth": {
+          "type": "boolean",
+          "title": "Skip depth normalization",
+          "default": false,
+          "description": "Skip depth normalization, this will make the pipeline slower."
         }
       }
     },
diff --git a/workflows/illuminaMpxv.nf b/workflows/illuminaMpxv.nf
index 1ea7129..0fadda8 100644
--- a/workflows/illuminaMpxv.nf
+++ b/workflows/illuminaMpxv.nf
@@ -69,13 +69,13 @@ workflow sequenceAnalysis {
 
     main:
 
-      // if (!params.skip_normalize_depth) {
-      //   ch_reads_to_hostfilter = normalizeDepth(ch_filePairs)
-      // } else {
-      //   ch_reads_to_hostfilter = ch_filePairs
-      // }
+      if (!params.skip_normalize_depth) {
+        ch_reads_to_hostfilter = normalizeDepth(ch_filePairs)
+      } else {
+        ch_reads_to_hostfilter = ch_filePairs
+      }
 
-      performHostFilter(ch_filePairs)
+      performHostFilter(ch_reads_to_hostfilter)
 
       readTrimming(performHostFilter.out.fastqPairs)