Merge pull request #141 from CDCgov/v1.6.3

v1.6.3

Author: zmudge3

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## v1.6.3 - [07/25/2025]
+### Fixed
+- [Pre-MycoSNP workflow] GC content calculation for closest GAMBIT match (`Reference_GC` field in pre-mycosnp-summary.csv) excluded lowercase (soft-masked) bases, i.e. "c" and "g", leading to underestimates for `Reference_GC`. This fix includes lowercase "g" and "c" in the GC content calculation in `bin/pre-mycosnp-stats.sh`, for both the closest GAMBIT match and the sample assembly. However, the sample assembly shouldn't contain any soft-masked bases to begin with, so this shouldn't result in any differences in `Sample_Assembly_GC`.
+
 ## v1.6.2 - [05/18/2025]
 ### Fixed
 - Docker permissions issue with GAMBIT container in some Linux environments (issue [#137](https://github.com/CDCgov/mycosnp-nf/issues/137))

bin/pre-mycosnp-stats.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-# pre-mycosnp-stats.sh v1.1.0
+# pre-mycosnp-stats.sh v1.1.1
 # Authors:
 # Jared Johnson, [email protected]
 # Zack Mudge, [email protected]
 
-version="v1.1.0"
+version="v1.1.1"
 
 #----- HELP & VERSION -----#
 # help message
@@ -72,7 +72,7 @@ if [[ -n "$ref" ]]; then # Check if ref is provided (not empty)
     ref_length=$(cat "${ref%.gz}" | grep -v ">" | tr -d '\n\t\r ' | wc -c)
 
     # reference %GC, to 2 decimal places
-    ref_gc_count=$(cat "${ref%.gz}" | grep -v ">" | grep -Eo "G|C" | wc -l)
+    ref_gc_count=$(cat "${ref%.gz}" | grep -v ">" | grep -Eo "G|C|g|c" | wc -l)
     ref_gc_perc=$(echo -e "${ref_gc_count}\t${ref_length}" | awk '{printf "%.2f", 100*$1/$2}')
 
     # estimated average depth of coverage, to 1 decimal place
@@ -85,7 +85,7 @@ else
 fi
 
 # sample assembly % GC, to 2 decimal places
-sample_gc_count=$(cat "${assembly%.gz}" | grep -v ">" | grep -Eo "G|C" | wc -l)
+sample_gc_count=$(cat "${assembly%.gz}" | grep -v ">" | grep -Eo "G|C|g|c" | wc -l)
 sample_gc_perc=$(echo -e "${sample_gc_count}\t${sample_length}" | awk '{printf "%.2f", 100*$1/$2}')
 
 #----- OUTPUT -----#

docs/output.md

@@ -99,7 +99,7 @@ Output files: `combined/pre-mycosnp_summary/pre-mycosnp-summary.csv`
 | Sample_Assembly_GC               | GC percentage of Shovill assembly                                                           |                                                      |
 | Reference_Genome_Length          | Length of the reference genome of the closest GAMBIT entry (if a prediction is made)        |                                                      |
 | Avg_Depth_Coverage               | (Total trimmed bases / `Reference_Genome_Length`)                                           |                                                      |
-| Reference_GC                     | GC percentage of the reference genome of the closest GAMBIT entry (if a prediction is made) |                                                      |
+| Reference_GC                     | GC percentage of the reference genome of the closest GAMBIT entry (if a prediction is made). Includes soft-masked bases i.e. lowercase "g" and "c". | |
 
 ### MultiQC
 - Outputs follow the same [pattern described for the main MycoSNP workflow](#multiqc-1).

docs/params.md

@@ -7,7 +7,7 @@
   |\ | |__  __ /  ` /  \ |__) |__         }  {
   | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                         `._,._,'
-  CDCgov/mycosnp-nf v1.6.2
+  CDCgov/mycosnp-nf v1.6.3
 ------------------------------------------------------
 Typical pipeline command:
 

nextflow.config

@@ -230,7 +230,7 @@ manifest {
     description     = 'MycoSNP is a portable workflow for performing whole genome sequencing analysis of fungal organisms, including Candida auris. This method prepares the reference, performs quality control, and calls variants using a reference. MycoSNP generates several output files that are compatible with downstream analytic tools, such as those for used for phylogenetic tree-building and gene variant annotations.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '1.6.2'
+    version = '1.6.3'
 }
 
 // Load modules.config for DSL2 module specific options