From cb83b38b07e43619c3634ad856c6bdbe7b93c616 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 10 Apr 2024 16:52:13 +0100 Subject: [PATCH] adjust all_accession_complete value --- eva_submission/nextflow/accession_and_load.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/eva_submission/nextflow/accession_and_load.nf b/eva_submission/nextflow/accession_and_load.nf index f24ca6f..2f17782 100644 --- a/eva_submission/nextflow/accession_and_load.nf +++ b/eva_submission/nextflow/accession_and_load.nf @@ -127,7 +127,7 @@ workflow { sort_and_compress_vcf(accession_vcf.out.accession_done) csi_vcfs = sort_and_compress_vcf.out.compressed_vcf accessioned_files_to_rm = accession_vcf.out.accessioned_filenames - all_accession_complete = sort_and_compress_vcf.out.compressed_vcf + all_accession_complete = sort_and_compress_vcf.out.compressed_vcf.collect() } csi_index_vcf(csi_vcfs) copy_to_ftp(csi_index_vcf.out.csi_indexed_vcf.toList(), accessioned_files_to_rm.toList()) @@ -155,8 +155,8 @@ workflow { .splitCsv(header:true) .map{row -> tuple(file(row.vcf_file), row.db_name)} // the vcf_files_dbname give the link between input file and all_accession_complete is to ensure the - // accessioning has been completed - if (all_accession_complete){ + // accessioning has been completed for all input files + if (all_accession_complete) { import_accession(vcf_files_dbname, all_accession_complete, load_variants_vcf.out.variant_load_complete) } }