diff --git a/workflows/genome-assembly/bacterial-genome-assembly/.dockstore.yml b/workflows/genome-assembly/bacterial-genome-assembly/.dockstore.yml index 5cb433d914..bd8656660a 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/.dockstore.yml +++ b/workflows/genome-assembly/bacterial-genome-assembly/.dockstore.yml @@ -17,3 +17,5 @@ workflows: - name: Clea Siguret alternateName: clsiguret orcid: 0009-0005-6140-0379 + - name: Hugo Lefeuvre + orcid: 0009-0005-6834-4058 diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md index d5bca11377..cb5a34c219 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md +++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md @@ -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 diff --git a/workflows/genome-assembly/bacterial-genome-assembly/README.md b/workflows/genome-assembly/bacterial-genome-assembly/README.md index 732a914bcb..1b616dedd8 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/README.md +++ b/workflows/genome-assembly/bacterial-genome-assembly/README.md @@ -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** diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml index 3da661c1e7..2e57cc1115 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml @@ -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)" diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga index b993b226fb..71ce05c1ae 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga @@ -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.", @@ -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": [] }, @@ -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": [] }, @@ -109,7 +117,7 @@ "name": "library" } ], - "label": "shovill_genome_assembly", + "label": "Shovill genome assembly", "name": "Shovill", "outputs": [ { @@ -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" } ] }, @@ -245,7 +253,7 @@ } }, "inputs": [], - "label": "bandage_contig_graph_stats", + "label": "Bandage contig graph stats", "name": "Bandage Info", "outputs": [ { @@ -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" } ] }, @@ -305,7 +313,7 @@ } }, "inputs": [], - "label": "bandage_contig_graph_plot", + "label": "Bandage contig graph plot", "name": "Bandage Image", "outputs": [ { @@ -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": [], @@ -390,8 +382,8 @@ } ], "position": { - "left": 1160.4198291830312, - "top": 32.46775364572329 + "left": 1116.121721297883, + "top": 61.60416487623325 }, "post_job_actions": { "RenameDatasetActionoutput_json": { @@ -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": { @@ -455,8 +447,8 @@ } ], "position": { - "left": 1443.4708168755199, - "top": 391.93805892524165 + "left": 1355.983929150398, + "top": 346.47653923847076 }, "post_job_actions": { "RenameDatasetActionsummary_json": { @@ -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" } ] } @@ -506,5 +498,5 @@ ], "uuid": "14fc2baa-a9fb-4e90-a8ec-f542faf1d8c2", "version": 1, - "release": "2.0" + "release": "2.0.1" } \ No newline at end of file