ABRicate task has been updated. It could still be used for other databases & applications, but when applied in these 2 workflows (illumina PE and SE) it is specific to the custom Acinetobacter baumannii plasmid typing database.
added commands for listing of available databases and dependency checking for logging purposes
added --threads ~{cpu} and --nopath to abricate command
added new string output for list of genes identified abricate_genes, separated by commas. Also can be a helpful string if no genes are found: "No genes detected by ABRicate"
new output string: abricate_docker
For both TheiaProk_illumina_PE and TheiaProk_illumina_SE, this task is now called if GAMBIT predicts a taxon of Acinetobacter baumannii. It uses a custom database of Acinetobacter baumannii plasmid rep genes which are used for typing. Default percent ID for this database is set to 95% to ensure match is really a match (for typing purposes).
The 5 outputs have also been added to the export_taxon_tables task and obviously the 2 workflows.
Both PE and SE workflows tested great in Terra on 5 samples.
Ready for testing & review!
Related to issue #99
ABRicate task has been updated. It could still be used for other databases & applications, but when applied in these 2 workflows (illumina PE and SE) it is specific to the custom Acinetobacter baumannii plasmid typing database.
tasks/gene_typing/task_abricate.wdlchanges:cpunow optional input param set to2staphb/abricate:1.0.1-abaum-plasmid. More info on docker image here.--threads ~{cpu}and--nopathtoabricatecommandabricate_genes, separated by commas. Also can be a helpful string if no genes are found:"No genes detected by ABRicate"abricate_dockerFor both TheiaProk_illumina_PE and TheiaProk_illumina_SE, this task is now called if GAMBIT predicts a taxon of
Acinetobacter baumannii. It uses a custom database of Acinetobacter baumannii plasmid rep genes which are used for typing. Default percent ID for this database is set to 95% to ensure match is really a match (for typing purposes).The 5 outputs have also been added to the
export_taxon_tablestask and obviously the 2 workflows.Both PE and SE workflows tested great in Terra on 5 samples.