diff --git a/eva_submission/eload_ingestion.py b/eva_submission/eload_ingestion.py index 3a2f6b8..ff1014d 100644 --- a/eva_submission/eload_ingestion.py +++ b/eva_submission/eload_ingestion.py @@ -166,7 +166,7 @@ def get_db_name(self, assembly_accession): """ # query EVAPRO for db name based on taxonomy id and accession with self.metadata_connection_handle as conn: - db_name = resolve_variant_warehouse_db_name(conn, assembly_accession, self.taxonomy) + db_name = resolve_variant_warehouse_db_name(conn, assembly_accession, self.taxonomy, ncbi_api_key=cfg.get('eutils_api_key')) if not db_name: raise ValueError(f'Database name for taxid:{self.taxonomy} and assembly {assembly_accession} ' f'could not be retrieved or constructed') diff --git a/eva_submission/etc/eva_project_conf.yaml b/eva_submission/etc/eva_project_conf.yaml index 4493444..29517bc 100644 --- a/eva_submission/etc/eva_project_conf.yaml +++ b/eva_submission/etc/eva_project_conf.yaml @@ -121,6 +121,7 @@ Sample: Title: string cultivar: string Description: string + Subject: string Files: required: diff --git a/eva_submission/etc/eva_project_validation.yaml b/eva_submission/etc/eva_project_validation.yaml index 426e914..c3bda10 100644 --- a/eva_submission/etc/eva_project_validation.yaml +++ b/eva_submission/etc/eva_project_validation.yaml @@ -106,7 +106,7 @@ Sample: cell_line: { type: 'string', nullable: True} serotype: { type: 'string', nullable: True} serovar: { type: 'string', nullable: True} - Novel attribute(s): { type: 'string', nullable: True, regex: '[\w.\-]+:[\w.\-]+(,\s*[\w.\-]+:[\w.\-]+)*'} + Novel attribute(s): { type: 'string', nullable: True, regex: '[\w.\-_ ]+:[\w.\-_ ]+(,\s*[\w.\-_ ]+:[\w.\-_ ]+)*'} Files: type: 'list' diff --git a/eva_submission/nextflow/accession_and_load.nf b/eva_submission/nextflow/accession_and_load.nf index 33576e1..516b434 100644 --- a/eva_submission/nextflow/accession_and_load.nf +++ b/eva_submission/nextflow/accession_and_load.nf @@ -214,6 +214,8 @@ process accession_vcf { clusterOptions "-o $params.logs_dir/${log_filename}.log \ -e $params.logs_dir/${log_filename}.err" + maxForks 1 + input: tuple val(vcf_filename), val(vcf_file), val(assembly_accession), val(aggregation), val(fasta), val(report)