Update bacterial_genome_annotation WF#1099
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SantaMcCloud wants to merge 7 commits intogalaxyproject:mainfrom
Open
Update bacterial_genome_annotation WF#1099SantaMcCloud wants to merge 7 commits intogalaxyproject:mainfrom
SantaMcCloud wants to merge 7 commits intogalaxyproject:mainfrom
Conversation
Author
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Hello @clsiguret and @hugolefeuvre, I made some modifications to your workflow, which still keep the original work. The only little changes i did are that Tooldistillator is now optional to run, and that some Bakta outputs are formatted and put together. These changes are made because we would like to use your WF in a different WF. @paulzierep or @bebatut can give you more details to this if there are any question! |
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Author
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hm idk why this is failing i did run this wihtout error |
Collaborator
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Hello, thank you for these changes. |
Author
Oh okay i can unterstand this. I can have a look and a talk with @paulzierep and @bebatut for keeping the single input instead of a collection. Otherwise beside of this if all the other changes would be fine to do this would be nice! The 2 new steps which work with the bakta output can be run with a single input aswell. Only the last step will create a single file from the whole collection this also can be done outside of the workflow so we can work around with it and remove it as a current change to the workflow so only the text reformat step would still be added to the workflow as change. |
Collaborator
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Thanks, please keep us informed on the progress. If the collection aspect is delayed, that will be fine with us. |
Removed assertions for MultiQC report text in tests.
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Collaborator
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@mvdbeek any idea what could be the issue here, all jobs are ok ? |
Author
@paulzierep i did run the current WF without any changes localy as test and even there planmeo was unable to finish the test and find somehow |
Collaborator
You mean the original one, that is already merged ? |
Author
Yes i will open a PR with it to check it |
Author
Author
Okay in GitHub the test runs fine strange. I will change the WF step by step then to see where the error come from |
Member
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Nothing's changed, and I'm not seeing what's wrong here. |
Contributor
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Pull request overview
This PR updates the bacterial genome annotation workflow to version 1.2.1, adding new features for conditional ToolDistillator execution and MultiQC report generation, while changing the input type from a single dataset to a collection.
Changes:
- Input changed from single FASTA file to sequence collection for processing multiple samples
- Added three new boolean input parameters to control ToolDistillator execution with/without Bakta
- Integrated MultiQC tool for aggregating Bakta output and new column join tool for merging Bakta annotation summaries
- Reordered workflow steps and adjusted tool connections accordingly
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
| bacterial_genome_annotation.ga | Main workflow file with input type change, new conditional parameters, new tools (MultiQC, text reformatting, column join), and reordered step IDs |
| bacterial_genome_annotation-tests.yml | Updated test inputs to use collection format and added tests for new outputs |
| CHANGELOG.md | Version bump to 1.2.1 with description of new features |
Comments suppressed due to low confidence (1)
workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga:1577
- The workflow_outputs labels use underscores which violates IWC naming conventions. These labels should use spaces instead of underscores. For example: "ToolDistillator results annotation without Bakta", "MultiQC HTML report", "Bakta cut annotation summary", "ToolDistillator results annotation Bakta", "ToolDistillator summarize Bakta", "Bakta annotation JSON", "ToolDistillator summarize annotation without Bakta".
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"output_name": "output_json",
"uuid": "36a3e2bf-f0ee-4f62-947c-02ae5c6ebb94"
}
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"inputs": [],
"label": "Format Bakta output",
"name": "Text reformatting",
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{
"name": "outfile",
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"when": "$(inputs.when)",
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{
"label": "bakta_annotation_json",
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{
"name": "html_report",
"type": "html"
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{
"name": "stats",
"type": "tabular"
}
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"label": "multiqc_html_report",
"output_name": "html_report",
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"annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file",
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"output_name": "output_json"
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"inputs": [],
"label": "ToolDistillator summarize without bakta",
"name": "ToolDistillator Summarize",
"outputs": [
{
"name": "summary_json",
"type": "json"
}
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"top": 667.0155177682022
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"RenameDatasetActionsummary_json": {
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"newname": "tooldistillator_summarize_annotation_without_bakta"
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"output_name": "summary_json"
},
"TagDatasetActionsummary_json": {
"action_arguments": {
"tags": "tooldistillator_summarize_annotation_without_bakta"
},
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"tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "1.0.4+galaxy0",
"type": "tool",
"uuid": "26ac168e-b283-494c-b335-fdacc8ae787e",
"when": "$(inputs.when)",
"workflow_outputs": [
{
"label": "tooldistillator_summarize_annotation_without_bakta",
"output_name": "summary_json",
"uuid": "81fbb555-99c3-4db5-a5dc-b669cb370828"
}
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"16": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
"errors": null,
"id": 16,
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"input_tabular": {
"id": 12,
"output_name": "outfile"
},
"when": {
"id": 5,
"output_name": "output"
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},
"inputs": [],
"label": "Merge Bakta Output",
"name": "Column join",
"outputs": [
{
"name": "tabular_output",
"type": "tabular"
}
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"top": 2164.354340453003
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"TagDatasetActiontabular_output": {
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"output_name": "tabular_output"
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"tool_uuid": null,
"tool_version": "0.0.3",
"type": "tool",
"uuid": "d5b93d1c-b5d5-422c-9ade-d604a3da2d5c",
"when": "$(inputs.when)",
"workflow_outputs": [
{
"label": "bakta_cut_annotation_summary",
"output_name": "tabular_output",
"uuid": "308b008d-c23c-4769-bcdf-0d443101c508"
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"17": {
"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/1.0.4+galaxy0",
"errors": null,
"id": 17,
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"tool_section|tools_0|select_tool|annotation_genbank_path": {
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"output_name": "annotation_tsv"
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"tool_section|tools_0|select_tool|input": {
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"when": {
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"output_name": "output"
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},
"inputs": [],
"label": "ToolDistillator bakta",
"name": "ToolDistillator",
"outputs": [
{
"name": "output_json",
"type": "input"
}
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"name": "ToolDistillator Summarize",
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"type": "json"
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| "3": { | ||
| "annotation": "Select a database to annotate AMR genes with Bakta.", | ||
| "annotation": "", | ||
| "content_id": null, | ||
| "errors": null, | ||
| "id": 3, | ||
| "input_connections": {}, | ||
| "inputs": [ | ||
| { | ||
| "description": "Select a database to annotate AMR genes with Bakta.", | ||
| "name": "AMRFinderPlus database" | ||
| "description": "", | ||
| "name": "Run ToolDistillator without bakta" | ||
| } | ||
| ], | ||
| "label": "AMRFinderPlus database", | ||
| "label": "Run ToolDistillator without bakta", | ||
| "name": "Input parameter", | ||
| "outputs": [], | ||
| "position": { | ||
| "left": 10.643158620281753, | ||
| "top": 995.2631409484753 | ||
| "left": 1428.993485907075, | ||
| "top": 0 | ||
| }, | ||
| "tool_id": null, | ||
| "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", | ||
| "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", | ||
| "tool_version": null, | ||
| "type": "parameter_input", | ||
| "uuid": "aec02a2c-6bf7-476d-91aa-3f1ce49083c7", | ||
| "uuid": "1c62baa7-8878-4480-b935-55d2eee80ada", | ||
| "when": null, | ||
| "workflow_outputs": [] | ||
| }, | ||
| "4": { | ||
| "annotation": "Choose if you want to run bakta or not (can take a long time)", | ||
| "annotation": "", | ||
| "content_id": null, | ||
| "errors": null, | ||
| "id": 4, | ||
| "input_connections": {}, | ||
| "inputs": [ | ||
| { | ||
| "description": "", | ||
| "name": "Run ToolDistillator with only bakta" | ||
| } | ||
| ], | ||
| "label": "Run ToolDistillator with only bakta", | ||
| "name": "Input parameter", | ||
| "outputs": [], | ||
| "position": { | ||
| "left": 1097.9011758567576, | ||
| "top": 1345.2437424956506 | ||
| }, | ||
| "tool_id": null, | ||
| "tool_state": "{\"validators\": [], \"parameter_type\": \"boolean\", \"optional\": false}", | ||
| "tool_version": null, | ||
| "type": "parameter_input", | ||
| "uuid": "830820e8-9d45-4ae5-8c4b-ea9f51c0edd5", | ||
| "when": null, | ||
| "workflow_outputs": [] | ||
| }, |
There was a problem hiding this comment.
The new input parameters "Run ToolDistillator without bakta" and "Run ToolDistillator with only bakta" have empty annotation fields. According to IWC guidelines, inputs should have descriptive annotations explaining what they do. Please add descriptive annotations to explain the purpose of these parameters.
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| "workflow_outputs": [ | ||
| { | ||
| "label": "plasmidfinder_hit_genome_fasta", | ||
| "output_name": "hit_file", | ||
| "uuid": "2924588e-064d-4c31-9011-ef9cfc646c6e" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_results_tabular", | ||
| "output_name": "result_file", | ||
| "uuid": "696867f7-0700-4ca5-bee4-bf405f44f6fa" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_result_json", | ||
| "output_name": "json_file", | ||
| "uuid": "1449c8c3-9621-4ba2-b32e-29a597a63f2d" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_hit_reference_fasta", | ||
| "output_name": "plasmid_file", | ||
| "uuid": "b70ea191-97da-4e59-b14c-3988284e552e" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_results_raw", | ||
| "output_name": "raw_file", | ||
| "uuid": "e4c42f08-1e32-40e0-a0f0-09037299c4a7" | ||
| } | ||
| ] |
There was a problem hiding this comment.
The workflow_outputs labels use underscores which violates the IWC naming convention requirement. According to IWC guidelines, workflow inputs and outputs should have human-readable names with spaces, no underscores, and dashes only where spelling dictates. Labels like "plasmidfinder_hit_genome_fasta", "plasmidfinder_results_tabular", "isescan_results_tabular", etc. should be changed to use spaces instead of underscores. For example: "PlasmidFinder hit genome FASTA", "PlasmidFinder results tabular", "ISEScan results tabular", etc.
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| @@ -350,35 +571,35 @@ | |||
| "uuid": "a89b0159-ccef-4c10-9b17-d5da62312bda" | |||
| }, | |||
| { | |||
| "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_orf_fasta", | |||
| "output_name": "orf_fna", | |||
| "uuid": "1a91afd7-104d-4807-bffa-61c5df646b85" | |||
| "label": "isescan_logfile_text", | |||
| "output_name": "logfile", | |||
| "uuid": "c0539e24-831e-406f-a5d2-3dd52845a5d7" | |||
| }, | |||
| { | |||
| "label": "isescan_summary_tabular", | |||
| "output_name": "summary", | |||
| "uuid": "a09e2ed7-5b31-4beb-9923-d5ec6910da16" | |||
| }, | |||
| { | |||
| "label": "isescan_annotation_gff3", | |||
| "output_name": "annotation", | |||
| "uuid": "de82533b-90f8-470d-80a2-e1559be93f0d" | |||
| "label": "isescan_orf_fasta", | |||
| "output_name": "orf_fna", | |||
| "uuid": "1a91afd7-104d-4807-bffa-61c5df646b85" | |||
| } | |||
| ] | |||
There was a problem hiding this comment.
The workflow_outputs labels use underscores which violates IWC naming conventions. These should use spaces instead of underscores. For example: "ISEScan results tabular" instead of "isescan_results_tabular", "ISEScan ORF FAA" instead of "isescan_orf_faa", etc.
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| "workflow_outputs": [ | ||
| { | ||
| "label": "plasmidfinder_results_raw", | ||
| "output_name": "raw_file", | ||
| "uuid": "e4c42f08-1e32-40e0-a0f0-09037299c4a7" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_hit_genome_fasta", | ||
| "output_name": "hit_file", | ||
| "uuid": "2924588e-064d-4c31-9011-ef9cfc646c6e" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_results_tabular", | ||
| "output_name": "result_file", | ||
| "uuid": "696867f7-0700-4ca5-bee4-bf405f44f6fa" | ||
| "label": "integronfinder2_results_tabular", | ||
| "output_name": "integrons_table", | ||
| "uuid": "cb38191b-3a0e-43d3-823a-0c9563e39d66" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_result_json", | ||
| "output_name": "json_file", | ||
| "uuid": "1449c8c3-9621-4ba2-b32e-29a597a63f2d" | ||
| "label": "integronfinder2_summary", | ||
| "output_name": "summary", | ||
| "uuid": "b96d90c3-7678-41b8-9b01-61d5c9da80bc" | ||
| }, | ||
| { | ||
| "label": "plasmidfinder_hit_reference_fasta", | ||
| "output_name": "plasmid_file", | ||
| "uuid": "b70ea191-97da-4e59-b14c-3988284e552e" | ||
| "label": "integronfinder2_logfile_text", | ||
| "output_name": "integron_log", | ||
| "uuid": "dca60f87-9f7a-4631-b197-62ca54f7bafe" | ||
| } | ||
| ] |
There was a problem hiding this comment.
The workflow_outputs labels use underscores which violates IWC naming conventions. These should use human-readable names with spaces. For example: "IntegronFinder2 results tabular", "IntegronFinder2 summary", "IntegronFinder2 logfile text".
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| @@ -964,29 +1037,14 @@ | |||
| "label": "bakta_annotation_gbff", | |||
| "output_name": "annotation_gbff", | |||
| "uuid": "5a6c32eb-42ca-45c0-afc9-a12cc777247d" | |||
| }, | |||
| { | |||
| "label": "bakta_aminoacid_sequence_faa", | |||
| "output_name": "annotation_faa", | |||
| "uuid": "3827a853-ad2a-48ad-89dd-648883467abd" | |||
| }, | |||
| { | |||
| "label": "bakta_nucleotide_sequence_fasta", | |||
| "output_name": "annotation_ffn", | |||
| "uuid": "31d239a4-5065-49fb-9989-8b83f3b53642" | |||
| }, | |||
| { | |||
| "label": "bakta_annotation_gff3", | |||
| "output_name": "annotation_gff3", | |||
| "uuid": "3af64163-439d-4241-b950-f540e6f18134" | |||
| } | |||
| ] | |||
There was a problem hiding this comment.
The workflow_outputs labels use underscores which violates IWC naming conventions. These Bakta output labels should use human-readable names with spaces instead of underscores. For example: "Bakta aminoacid sequence FAA", "Bakta nucleotide sequence FASTA", "Bakta annotation GFF3", etc.
Test Results (powered by Planemo)Test Summary
Failed Tests
|
Author
|
Okay now i did know why the test didnt run correctly. My VSC did crash and some changes i did made in the test file wherent save or they where reverted....now evreything should be fine. |
Collaborator
hugolefeuvre
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hugolefeuvre
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Thank you for these changes ! A few comments regarding our previous discussions
| "inputs": [ | ||
| { | ||
| "description": "", | ||
| "name": "Sequence collection" |
Collaborator
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Would it be possible to revert to individual file mode, as agreed ?
| "workflow_outputs": [] | ||
| }, | ||
| "5": { | ||
| "6": { |
Collaborator
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For the WF to work properly on our end, we need the input brick for the input files to be in the first position. Would it be possible to put it back in the first position ?
| hashes: | ||
| - hash_function: SHA-1 | ||
| hash_value: b77e9cf8473eaba8a640a398a0b06b9c87249052 | ||
| Sequence collection: |
Collaborator
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Please remember to switch back to individual file mode.
| }, | ||
| "12": { | ||
| "16": { | ||
| "annotation": "", |
Collaborator
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Can you add an explanation about this step ?
| }, | ||
| "10": { | ||
| "12": { | ||
| "annotation": "", |
Collaborator
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Can you add a little explanation about this step ?
Collaborator
|
Looking at the workflow via the Galaxy interface, it seems that some connections related to conditionals are not connected correctly. This does not seem to cause any problems with the tests at the moment, but I wonder if it could cause problems later on. |
Collaborator
We think this is a workflow editor atrifact, it should be correct to connect those jobs and since the workflow actually works, we would ignore it for now, we should make an issue to galaxy, though. |
Collaborator
I suggest that workflows should be updated to reflect the latest developments, since they are intended for the broader Galaxy community. Can you not pin the Abromics workflow to use a specific version that works for you ? Otherwise I would propose to rename this workflow to something like: bacterial_genome_annotation_ABRomics since its only really makes sense in this context. No offence I totally get why its set up like this, but we should discuss policy here as a community. I will check in the IWC channel as well. |
Collaborator
I completely agree with you, the collection aspect is what we ultimately want to use, but for now we are not yet ready on the platform side. Yes, it is possible to specify a version, which is what we are doing, I believe, but if there is a switch to the collection in the next version and we want to make changes afterwards, i.e., a new version of the workflow, we will be stuck. No worries, I recognize that this isn't an ideal situation and that it would be easier to agree on a single workflow, but yes, I think renaming the workflow is still the simplest solution. I'm following the discussions on the channel. |
Collaborator
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I can use this WF as a basis to make a batch version but: 
Actually, I just realized that this WF (the initial one before this PR) is broken anyway, since if you do set run_bakta as false is fails. This is probably why Santino made the pick value step optional, which then makes the connection to the non-option input look strange. Strangely, the error of the pick value tool if no input is provided is: 
@mvdbeek is this a bug of the pick value tool ? it should return null, or is this showing the downstream tool, but it should not run with a null input ? |
Collaborator
This might be a EU specific issue, need to check. |
Collaborator
It normally works fine on the FR server; the platform developers have not reported this type of error. |
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FOR CONTRIBUTOR:
FOR REVIEWERS:
This workflow does/runs/performs … xyz … to generate/analyze/etc …namefield should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id