Merge pull request #395 from UPHL-BioNGS/patch-fix

Patch fix
UPHL-BioNGS · Dec 12, 2024 · 5d96130 · 5d96130
2 parents 9017340 + 5035100
commit 5d96130
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git 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
@@ -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
-}
+}