add more reads globs

UPHL-BioNGS · Dec 11, 2024 · 6076c01 · 6076c01
1 parent 9017340
commit 6076c01
Showing 1 changed file with 3 additions and 2 deletions.
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
-}
+}