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Update bakta paramter as requested in MAG WF #1326

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Update bakta paramter as requested in MAG WF #1326

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4 changes: 4 additions & 0 deletions workflows/microbiome/mag-genome-annotation-parallel/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Changelog

## [0.5] - 2026-07-29

- Modify two of the default parameters for bakta. Bakta now always operates in metagenome mode, and the input header is retained for the output.

## [0.4] - 2026-07-20

### Automatic update
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66 changes: 33 additions & 33 deletions workflows/microbiome/mag-genome-annotation-parallel/MAG-Genome-Annotation-Parallel.ga
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Original file line number Diff line number Diff line change
Expand Up @@ -532,14 +532,9 @@
"when": null,
"workflow_outputs": [
{
"label": "isescan orf fasta",
"output_name": "orf_fna",
"uuid": "1a91afd7-104d-4807-bffa-61c5df646b85"
},
{
"label": "isescan results tabular",
"output_name": "all_results",
"uuid": "24f7dee0-f50a-4444-83f4-b09623a4a993"
"label": "isescan annotation gff3",
"output_name": "annotation",
"uuid": "de82533b-90f8-470d-80a2-e1559be93f0d"
},
{
"label": "isescan is fasta",
Expand All @@ -556,15 +551,20 @@
"output_name": "logfile",
"uuid": "c0539e24-831e-406f-a5d2-3dd52845a5d7"
},
{
"label": "isescan annotation gff3",
"output_name": "annotation",
"uuid": "de82533b-90f8-470d-80a2-e1559be93f0d"
},
{
"label": "isescan summary tabular",
"output_name": "summary",
"uuid": "a09e2ed7-5b31-4beb-9923-d5ec6910da16"
},
{
"label": "isescan orf fasta",
"output_name": "orf_fna",
"uuid": "1a91afd7-104d-4807-bffa-61c5df646b85"
},
{
"label": "isescan results tabular",
"output_name": "all_results",
"uuid": "24f7dee0-f50a-4444-83f4-b09623a4a993"
}
]
},
Expand Down Expand Up @@ -664,19 +664,19 @@
"when": null,
"workflow_outputs": [
{
"label": "integronfinder2 summary",
"output_name": "summary",
"uuid": "b96d90c3-7678-41b8-9b01-61d5c9da80bc"
"label": "integronfinder2 results tabular",
"output_name": "integrons_table",
"uuid": "cb38191b-3a0e-43d3-823a-0c9563e39d66"
},
{
"label": "integronfinder2 logfile text",
"output_name": "integron_log",
"uuid": "dca60f87-9f7a-4631-b197-62ca54f7bafe"
},
{
"label": "integronfinder2 results tabular",
"output_name": "integrons_table",
"uuid": "cb38191b-3a0e-43d3-823a-0c9563e39d66"
"label": "integronfinder2 summary",
"output_name": "summary",
"uuid": "b96d90c3-7678-41b8-9b01-61d5c9da80bc"
}
]
},
Expand Down Expand Up @@ -819,6 +819,11 @@
"uuid": "0cbd7d74-9525-4fc4-9518-836c99f6d397",
"when": null,
"workflow_outputs": [
{
"label": "plasmidfinder hit reference fasta",
"output_name": "plasmid_file",
"uuid": "b70ea191-97da-4e59-b14c-3988284e552e"
},
{
"label": "plasmidfinder result json",
"output_name": "json_file",
Expand All @@ -838,11 +843,6 @@
"label": "plasmidfinder results raw",
"output_name": "raw_file",
"uuid": "e4c42f08-1e32-40e0-a0f0-09037299c4a7"
},
{
"label": "plasmidfinder hit reference fasta",
"output_name": "plasmid_file",
"uuid": "b70ea191-97da-4e59-b14c-3988284e552e"
}
]
},
Expand Down Expand Up @@ -1118,13 +1118,18 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": false, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": false, \"regions\": {\"__class__\": \"RuntimeValue\"}}, \"input_option\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null, \"bakta_db_select\": {\"__class__\": \"ConnectedValue\"}, \"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"file_gbff\", \"file_embl\", \"file_fna\", \"file_faa\", \"hypo_tsv\", \"hypo_fa\", \"file_json\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": true, \"regions\": {\"__class__\": \"RuntimeValue\"}}, \"input_option\": {\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"min_contig_length\": null, \"bakta_db_select\": {\"__class__\": \"ConnectedValue\"}, \"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"file_gbff\", \"file_embl\", \"file_fna\", \"file_faa\", \"hypo_tsv\", \"hypo_fa\", \"file_json\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "1.9.4+galaxy1",
"type": "tool",
"uuid": "0a32dcad-f456-460e-9e6f-9e306a8fd515",
"when": "$(inputs.when)",
"workflow_outputs": [
{
"label": "bakta annotation gff3",
"output_name": "annotation_gff3",
"uuid": "3af64163-439d-4241-b950-f540e6f18134"
},
{
"label": "bakta nucleotide sequence fasta",
"output_name": "annotation_ffn",
Expand Down Expand Up @@ -1174,11 +1179,6 @@
"label": "bakta annotation tabular",
"output_name": "annotation_tsv",
"uuid": "b84d6b52-d921-42d5-a7df-4abbd523bdc7"
},
{
"label": "bakta annotation gff3",
"output_name": "annotation_gff3",
"uuid": "3af64163-439d-4241-b950-f540e6f18134"
}
]
},
Expand Down Expand Up @@ -1537,7 +1537,7 @@
}
},
"tags": [],
"uuid": "9b1e5eb3-e343-48de-bcc4-409788e7375c"
"uuid": "a7d5975c-a3a7-4d96-a28c-c570b11d8cb9"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -2054,7 +2054,7 @@
}
},
"tags": [],
"uuid": "3db8aa4f-2428-44e1-a552-873270452211",
"uuid": "eae970a3-553b-435f-accf-b5db354e93cf",
"version": 1,
"release": "0.4"
"release": "0.5"
}
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