Fixed FASTQ regex to account for sequencers without discrete lanes

TheJacksonLaboratory · Oct 26, 2021 · 76a8110 · 76a8110
1 parent 0d39ecb
commit 76a8110
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/functions.nf b/modules/functions.nf
@@ -48,7 +48,7 @@ def collect_fastqs(record) {
         fastq -> if(fastq =~ /$lib/) { 
            if (!(fastq in fastqs)) { fastqs.add(fastq.toString()) }
            // everything before S\d+_L\d+_[IR]\d+_001.fastq.gz
-           prefix = (file(fastq).getName() =~ /(.*)_S\d+_L\d+_[IR]\d+_001.fastq.gz/)[0][1]
+           prefix = (file(fastq).getName() =~ /(.*)_S\d+_(L\d+_)?[IR]\d+_001.fastq.gz/)[0][1]
            if (!(prefix in prefixes)) { prefixes.add(prefix) }
         }
       }