From 7ed9164b8ae525b4a50da0ad0611401da00c002e Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Fri, 23 Jun 2023 09:31:42 -0700
Subject: [PATCH] Allow normalizeDepth process to be skipped (#16)

---
 README.md                 |  2 ++
 nextflow.config           |  5 ++++-
 workflows/illuminaMpxv.nf | 10 +++++++---
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index cedb83b..19f1da0 100644
--- a/README.md
+++ b/README.md
@@ -75,6 +75,8 @@ Important config options are:
 | `varFreqThreshold`               | `0.75`   | Allele frequency threshold for unambiguous variant                                                                  |
 | `varMinDepth`                    | `10`     | Minimum coverage depth to call variant                                                                              |
 
+### Depth Normalization
+By default, sequence depth will be normalized using `bbnorm` to the value specified by the `--normalizationTargetDepth` param (default: 200). To skip depth normalization, add the `--skip_normalize_depth` flag.
 
 #### QC
 A script to do some basic QC is provided in `bin/qc.py`. It measures the % of reference bases are covered by `varMinDepth`, and the longest stretch of consensus sequence with no `N` bases. This script does not make a QC pass/fail call.
diff --git a/nextflow.config b/nextflow.config
index 45490ca..4363fa1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -35,7 +35,10 @@ params {
   help = false
   outdir = './results'
   tracedir = "${params.outdir}/pipeline_info"
-  
+
+  // depth normalization
+  skip_normalize_depth = false
+
   // host filtering
   composite_ref = false
   viral_contig_name = 'NC_063383.1'
diff --git a/workflows/illuminaMpxv.nf b/workflows/illuminaMpxv.nf
index 7d5a5ac..44875c6 100644
--- a/workflows/illuminaMpxv.nf
+++ b/workflows/illuminaMpxv.nf
@@ -3,8 +3,8 @@
 nextflow.enable.dsl = 2
 
 include { articDownloadScheme }       from '../modules/utils.nf'
-include { performHostFilter }         from '../modules/illumina.nf'
 include { normalizeDepth }            from '../modules/illumina.nf'
+include { performHostFilter }         from '../modules/illumina.nf'
 include { readTrimming }              from '../modules/illumina.nf'
 include { filterResidualAdapters }    from '../modules/illumina.nf'
 include { indexReference }            from '../modules/illumina.nf'
@@ -88,9 +88,13 @@ workflow sequenceAnalysis {
 
     main:
 
-      normalizeDepth(ch_filePairs)
+      if (!params.skip_normalize_depth) {
+        ch_reads_to_hostfilter = normalizeDepth(ch_filePairs)
+      } else {
+        ch_reads_to_hostfilter = ch_filePairs
+      }
 
-      performHostFilter(normalizeDepth.out)
+      performHostFilter(ch_reads_to_hostfilter)
 
       readTrimming(performHostFilter.out.fastqPairs)