diff --git a/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf b/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf index cb5e2b8..9140cea 100644 --- a/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf +++ b/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf @@ -43,8 +43,9 @@ process GET_RUN_ACCESSIONS { script: runAccessionList = [] runAccessionToFile='run_accession_list.txt' - def fileBatch=new File(run_accession_batch) - if (fileBatch.exists()){ + //def fileBatch=new File(run_accession_batch) + //if (fileBatch.exists()){ + if (run_accession_batch && file(run_accession_batch).exists()){ fileBatch.eachLine { line -> runAccessionList.add([taxon_id: taxon_id, gca: gca, run_accession: line]) }