galaxyproject / galaxyproject/galaxy_codex

Add workflow input / output files

Open
#572 4 comments 0 reactions 0 assignees Claimed by @paulzierep View on GitHub
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HTML
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28
Forks
36
Avg merge
19h 29m
Merged PRs (30d)
1

Description

There was a request to add input output information to a workflow, file type would be useful.
But a quick check showed that the information that can be requested form workflowhub is not very useful imo.
For some reason file type is not included.

```python
import json

for wf in data:
wfhub_wf = get_request_json(
f"https://{prefix}workflowhub.eu{wf['links']['self']}",
header,
)

internals = wfhub_wf["data"]["attributes"]["internals"]

io = {
"inputs": internals.get("inputs", []),
"outputs": internals.get("outputs", []),
}

print(json.dumps(io, indent=2))
break
```

Output

```
{
"inputs": [
{
"id": "#main/Bacterial genome contigs",
"name": "#main/Bacterial genome contigs",
"description": "The input for this workflow is a single FASTA file containing contigs of one bacterial genome.",
"type": [
{
"type": "File"
}
],
"default_value": null
},
{
"id": "#main/Reference Allele Scheme",
"name": "#main/Reference Allele Scheme",
"description": "Reference Allele Scheme (from pubMLST, BIGSdb, Enterobase, or cgMLST.org) that will be used by CoreProfiler to compare the contigs to and identify corresponding alleles.",
"type": [
{
"type": "string"
}
],
"default_value": null
}
],
"outputs": [
{
"id": "#main/CoreProfiler allele calling report",
"name": "#main/CoreProfiler allele calling report",
"description": null,
"type": [
{
"type": "File"
}
],
"source_ids": [
"#main/CoreProfiler/output_file"
]
},
{
"id": "#main/Extracted cgMLST results by ToolDistillator",
"name": "#main/Extracted cgMLST results by ToolDistillator",
"description": null,
"type": [
{
"type": "File"
}
],
"source_ids": [
"#main/ToolDistillator extraction/output_json"
]
},
{
"id": "#main/Information about temporary alleles found by CoreProfiler",
"name": "#main/Information about temporary alleles found by CoreProfiler",
"description": null,
"type": [
{
"type": "File"
}
],
"source_ids": [
"#main/CoreProfiler/profiles_w_tmp_alleles"
]
},
{
"id": "#main/Newly detected alleles by CoreProfiler",
"name": "#main/Newly detected alleles by CoreProfiler",
"description": null,
"type": [
{
"type": "File"
}
],
"source_ids": [
"#main/CoreProfiler/outfa"
]
},
{
"id": "#main/Summarized cgMLST ToolDistillator results",
"name": "#main/Summarized cgMLST ToolDistillator results",
"description": null,
"type": [
{
"type": "File"
}
],
"source_ids": [
"#main/ToolDistillator summarize/summary_json"
]
}
]
}

```

Contributor guide

Open the contributing guide

Research direction

Start by reviewing open pull request #701 and the WorkflowHub response shown in the issue, especially the internals inputs and outputs fields. Determine how workflow metadata is represented in the catalog and whether file types can be preserved; done means the requested input and output information is exposed with the available type data.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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