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Merged
mvdbeek merged 2 commits into from
Dec 3, 2025
Merged

Update bacterial genome assembly wf to 2.0.1 #1029

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b200bb1
update bacterial genome assembly wf to 2.0.1
hugolefeuvre Dec 1, 2025
81ded00
delete WIP on WF name
hugolefeuvre Dec 1, 2025
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2 changes: 2 additions & 0 deletions workflows/genome-assembly/bacterial-genome-assembly/.dockstore.yml
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Expand Up @@ -17,3 +17,5 @@ workflows:
- name: Clea Siguret
alternateName: clsiguret
orcid: 0009-0005-6140-0379
- name: Hugo Lefeuvre
orcid: 0009-0005-6834-4058
11 changes: 11 additions & 0 deletions workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
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@@ -1,5 +1,16 @@
# Changelog

## [2.0.1] - 2025-12-01

### Automatic update

- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0`

### Removed

* Remove some Tooldistillator input because the main information is not found in these files

## [2.0] - 2025-08-11

### Removed
Expand Down
2 changes: 1 addition & 1 deletion workflows/genome-assembly/bacterial-genome-assembly/README.md
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Expand Up @@ -23,4 +23,4 @@ This workflow uses paired-end illumina trimmed reads fastq(.gz) files and execut
- Assembly Graph
- Assembly report
3. Aggregating outputs
- JSON file with information about the outputs of **Shovill**, **Bandage**
- JSON file with information about the outputs of **Shovill**
4 changes: 0 additions & 4 deletions workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml
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Expand Up @@ -33,7 +33,3 @@
text: "\"Assembly\": \"shovill_contigs_fasta\""
has_text:
text: "contig00146"
has_text:
text: "bandage_plot_path"
has_text:
text: "Total_length_no_overlaps_(bp)"
88 changes: 40 additions & 48 deletions workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
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Expand Up @@ -24,11 +24,19 @@
"class": "Person",
"identifier": "https://orcid.org/0009-0005-6140-0379",
"name": "Clea Siguret"
},
{
"class": "Person",
"identifier": "https://orcid.org/0009-0005-6834-4058",
"name": "Hugo Lefeuvre"
}
],
"format-version": "0.1",
"license": "GPL-3.0-or-later",
"name": "Bacterial Genome Assembly using Shovill",
"report": {
"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
},
"steps": {
"0": {
"annotation": "Should be the adapter trimmed forward strand of the paired end reads.",
Expand All @@ -53,7 +61,7 @@
"tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "d223414b-29dc-4ffa-9851-a366cc4a3a80",
"uuid": "40f70938-12cb-4908-875a-28085631e951",
"when": null,
"workflow_outputs": []
},
Expand All @@ -80,7 +88,7 @@
"tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "33a6db62-4324-4469-a903-33b5ef505a17",
"uuid": "9542727a-8573-40b8-ad09-d0eb45231e3d",
"when": null,
"workflow_outputs": []
},
Expand Down Expand Up @@ -109,7 +117,7 @@
"name": "library"
}
],
"label": "shovill_genome_assembly",
"label": "Shovill genome assembly",
"name": "Shovill",
"outputs": [
{
Expand Down Expand Up @@ -208,28 +216,28 @@
"tool_state": "{\"adv\": {\"namefmt\": \"contig%05d\", \"depth\": \"100\", \"gsize\": \"\", \"kmers\": \"\", \"opts\": \"\", \"keep_files\": {\"nocorr\": \"yes_correction\", \"__current_case__\": 1, \"keepfiles\": true}, \"minlen\": \"0\", \"mincov\": \"2\"}, \"assembler\": \"spades\", \"library\": {\"lib_type\": \"paired\", \"__current_case__\": 0, \"R1\": {\"__class__\": \"ConnectedValue\"}, \"R2\": {\"__class__\": \"ConnectedValue\"}}, \"log\": true, \"trim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.0+galaxy2",
"type": "tool",
"uuid": "316380fb-2944-4d85-8832-8c8b70fe3623",
"uuid": "e7b73002-c415-445b-9e00-51f45caefe88",
"when": null,
"workflow_outputs": [
{
"label": "shovill_alignment_bam",
"output_name": "bamfiles",
"uuid": "8cbb3659-4de3-4c4f-b15d-c44dd5b5ccfa"
"uuid": "4d3aa9b6-a537-4897-b694-5b5095316a72"
},
{
"label": "shovill_contigs_graph",
"output_name": "contigs_graph",
"uuid": "d368ce7d-6123-436e-a566-a7ae0f56234d"
"uuid": "412b46ef-12e7-4597-8917-a6b327749f58"
},
{
"label": "shovill_logfile",
"output_name": "shovill_std_log",
"uuid": "3b25ebd4-8348-43ac-afdc-870e292d420e"
"uuid": "0013a7ae-d67d-4223-893f-9ef43182908d"
},
{
"label": "shovill_contigs_fasta",
"output_name": "contigs",
"uuid": "c74a1bd3-1a9e-45c2-aa00-4c42a6269eee"
"uuid": "817d1c97-960d-4d00-bc92-4692300dd4df"
}
]
},
Expand All @@ -245,7 +253,7 @@
}
},
"inputs": [],
"label": "bandage_contig_graph_stats",
"label": "Bandage contig graph stats",
"name": "Bandage Info",
"outputs": [
{
Expand Down Expand Up @@ -283,13 +291,13 @@
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2022.09+galaxy2",
"type": "tool",
"uuid": "e84778db-553a-424d-b71e-547994be4050",
"uuid": "9a92c323-4df3-4cb7-8ca6-abdf73de0ff3",
"when": null,
"workflow_outputs": [
{
"label": "bandage_contig_graph_stats",
"output_name": "outfile",
"uuid": "c075d076-3c99-48e2-94e9-ba9330c6c5f8"
"uuid": "db1a4fc2-5394-421c-a1a8-2907bec1c157"
}
]
},
Expand All @@ -305,7 +313,7 @@
}
},
"inputs": [],
"label": "bandage_contig_graph_plot",
"label": "Bandage contig graph plot",
"name": "Bandage Image",
"outputs": [
{
Expand Down Expand Up @@ -343,41 +351,25 @@
"tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"svg\", \"width\": \"1000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2022.09+galaxy4",
"type": "tool",
"uuid": "7a357116-66a1-46d7-9af2-14e7415ef19e",
"uuid": "4482449a-7009-475d-9095-5d08fd465fed",
"when": null,
"workflow_outputs": [
{
"label": "bandage_contig_graph_plot",
"output_name": "outfile",
"uuid": "eb9d5175-0589-4c3e-8373-ef9cafc72e1e"
"uuid": "883cb5ea-7305-4ce7-bf5d-702bbaa23037"
}
]
},
"5": {
"annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0",
"errors": null,
"id": 5,
"input_connections": {
"tool_section|tools_0|select_tool|bam_file_path": {
"id": 2,
"output_name": "bamfiles"
},
"tool_section|tools_0|select_tool|contig_graph_path": {
"id": 2,
"output_name": "contigs_graph"
},
"tool_section|tools_0|select_tool|input": {
"id": 2,
"output_name": "contigs"
},
"tool_section|tools_1|select_tool|bandage_plot_path": {
"id": 4,
"output_name": "outfile"
},
"tool_section|tools_1|select_tool|input": {
"id": 3,
"output_name": "outfile"
}
},
"inputs": [],
Expand All @@ -390,8 +382,8 @@
}
],
"position": {
"left": 1160.4198291830312,
"top": 32.46775364572329
"left": 1116.121721297883,
"top": 61.60416487623325
},
"post_job_actions": {
"RenameDatasetActionoutput_json": {
Expand All @@ -409,29 +401,29 @@
"output_name": "output_json"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "c6b5c2975e51",
"changeset_revision": "9f1c8dc0253e",
"name": "tooldistillator",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 36, \"input\": {\"__class__\": \"RuntimeValue\"}, \"contig_graph_path\": {\"__class__\": \"RuntimeValue\"}, \"bam_file_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"bandage\", \"__current_case__\": 4, \"input\": {\"__class__\": \"RuntimeValue\"}, \"bandage_plot_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": null}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0+galaxy1",
"tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 36, \"input\": {\"__class__\": \"RuntimeValue\"}, \"contig_graph_path\": {\"__class__\": \"RuntimeValue\"}, \"bam_file_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": null}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.4+galaxy0",
"type": "tool",
"uuid": "b6156c8e-5048-41e3-90d9-f9302734c3d1",
"uuid": "12e27969-f4a9-47c8-a561-d7145ac83a0a",
"when": null,
"workflow_outputs": [
{
"label": "tooldistillator_results_assembly",
"output_name": "output_json",
"uuid": "b24e9f04-9398-4bdd-8697-fd44ad8129b6"
"uuid": "a5890d50-4eb8-4941-8af7-8c2eb91e4cb6"
}
]
},
"6": {
"annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
Expand All @@ -455,8 +447,8 @@
}
],
"position": {
"left": 1443.4708168755199,
"top": 391.93805892524165
"left": 1355.983929150398,
"top": 346.47653923847076
},
"post_job_actions": {
"RenameDatasetActionsummary_json": {
Expand All @@ -474,23 +466,23 @@
"output_name": "summary_json"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "3d0223265277",
"changeset_revision": "f4f71128f097",
"name": "tooldistillator_summarize",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"summarize_data\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0+galaxy1",
"tool_version": "1.0.4+galaxy0",
"type": "tool",
"uuid": "3bbe0eba-b6bb-4d43-ab57-2b899b8112ae",
"uuid": "e12a9c8d-3bf6-4f7e-8007-ba25d5722ce2",
"when": null,
"workflow_outputs": [
{
"label": "tooldistillator_summarize_assembly",
"output_name": "summary_json",
"uuid": "dd58ac41-dd1b-4bac-84d5-2f594660ce2b"
"uuid": "ca314221-a603-4908-aa12-fbd6882a1586"
}
]
}
Expand All @@ -506,5 +498,5 @@
],
"uuid": "14fc2baa-a9fb-4e90-a8ec-f542faf1d8c2",
"version": 1,
"release": "2.0"
"release": "2.0.1"
}