Allow normalizeDepth process to be skipped (#16)

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.

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'

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)