restored pair paths

Ensembl · Aug 13, 2024 · ad46333 · ad46333
1 parent 0c44b94
commit ad46333
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/pipelines/nextflow/modules/process_run_accession_metadata/download_paired_fastqs.nf b/pipelines/nextflow/modules/process_run_accession_metadata/download_paired_fastqs.nf
@@ -58,6 +58,8 @@ process DOWNLOAD_PAIRED_FASTQS {
     if(!url1 || !url2 || !md5_1 || !md5_2){
             log.error("Metadata corrupted")
     }else{
+        def pair1Path = "${params.outDir}/$taxon_id/$run_accession/${run_accession}_1.fastq.gz"
+        def pair2Path = "${params.outDir}/$taxon_id/$run_accession/${run_accession}_2.fastq.gz"
         def retryCount = 0
         def maxRetries = 3
         def md5Match = false