diff --git a/nextflow.config b/nextflow.config
index d7efa24..d403b75 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -263,7 +263,7 @@ manifest {
   name              = 'UPHL-BioNGS/Cecret'
   author            = 'Erin Young'
   homePage          = 'https://github.com/UPHL-BioNGS/Cecret'
-  version           = 'v3.22.24345'
+  version           = 'v3.22.24346'
   defaultBranch     = 'master'
   recurseSubmodules = false
   description       = 'Reference-based consensus creation'
diff --git a/subworkflows/local/initialize.nf b/subworkflows/local/initialize.nf
index c450b01..07a8353 100755
--- a/subworkflows/local/initialize.nf
+++ b/subworkflows/local/initialize.nf
@@ -172,7 +172,8 @@ workflow INITIALIZE {
         // looking for paired-end fastq files
         if (params.reads) {
             Channel
-                .fromFilePairs(["${params.reads}/*{1,2}*.{fastq,fastq.gz,fq,fq.gz}"], size: 2 )
+                .fromFilePairs(["${params.reads}/*_R{1,2}*.{fastq,fastq.gz,fq,fq.gz}",
+                        "${params.reads}/*_{1,2}*.{fastq,fastq.gz,fq,fq.gz}"], size: 2 )
                 .unique()
                 .map { it ->
                     meta = [id:it[0].replaceAll(~/_S[0-9]+_L[0-9]+/,""), single_end:false] 
@@ -514,4 +515,4 @@ workflow INITIALIZE {
     kraken2_db          = ch_kraken2_db // channel: path
     scripts             = ch_scripts // channel: [scripts]
     nextclade_dataset   = ch_nextclade_dataset // channel: file
-}
\ No newline at end of file
+}