Fix file sorting with radix method

CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#697](https://github.com/nf-core/ampliseq/pull/697),[#699](https://github.com/nf-core/ampliseq/pull/699),[#713](https://github.com/nf-core/ampliseq/pull/713) - Template update for nf-core/tools version 2.13.1
 - [#711](https://github.com/nf-core/ampliseq/pull/711) - From r207 and onwards Archaea sequences were omitted when parsing GTDB databases. (This did not affect `sbdi-gtdb` databases, only `gtdb`.)
 - [#715](https://github.com/nf-core/ampliseq/pull/715) - Fix filtering vsearch clusters for high number of clusters
+- [#717](https://github.com/nf-core/ampliseq/pull/717) - Fix edge case for sorting file names by using radix method
 
 ### `Dependencies`
 

modules/local/dada2_denoising.nf

@@ -34,8 +34,8 @@ process DADA2_DENOISING {
         errF = readRDS("${errormodel[0]}")
         errR = readRDS("${errormodel[1]}")
 
-        filtFs <- sort(list.files("./filtered/", pattern = "_1.filt.fastq.gz", full.names = TRUE))
-        filtRs <- sort(list.files("./filtered/", pattern = "_2.filt.fastq.gz", full.names = TRUE))
+        filtFs <- sort(list.files("./filtered/", pattern = "_1.filt.fastq.gz", full.names = TRUE), method = "radix")
+        filtRs <- sort(list.files("./filtered/", pattern = "_2.filt.fastq.gz", full.names = TRUE), method = "radix")
 
         #denoising
         sink(file = "${prefix}.dada.log")

modules/local/dada2_err.nf

@@ -32,8 +32,8 @@ process DADA2_ERR {
         suppressPackageStartupMessages(library(dada2))
         set.seed($seed) # Initialize random number generator for reproducibility
 
-        fnFs <- sort(list.files(".", pattern = "_1.filt.fastq.gz", full.names = TRUE))
-        fnRs <- sort(list.files(".", pattern = "_2.filt.fastq.gz", full.names = TRUE))
+        fnFs <- sort(list.files(".", pattern = "_1.filt.fastq.gz", full.names = TRUE), method = "radix")
+        fnRs <- sort(list.files(".", pattern = "_2.filt.fastq.gz", full.names = TRUE), method = "radix")
 
         sink(file = "${prefix}.err.log")
         errF <- learnErrors(fnFs, $args, multithread = $task.cpus, verbose = TRUE)