feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input.

[Smeds]

updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input.

[mvdbeek]

Nice! Can you take a look at https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows ?

[Smeds]

Nice! Can you take a look at https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#adding-workflows ?

Thanks! I will read through the readme and update the workflow.

[Delphine-L]

Need to solve galaxyproject/galaxy#19143 as soon as possible to settle on a way to deal with compressed haplotypes inputs

[Delphine-L]

I am not sure why the tests are not running. Could someone take a look ?

[mvdbeek]

I assume that's the reason ?

[mvdbeek]

we can merge this, but I'd urge you to think of better folder and workflow names. if you look at https://github.com/orgs/iwc-workflows/repositories?type=all most folders/repos are all-lowercase, I think that looks much nicer once we publish that to https://iwc.galaxyproject.org/.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	0
Passed	0
Error	0
Failure	0
Skipped	0

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ hi-c-map-for-assembly-manual-curation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '49' (Haplotype 2) is not optional and no input provided.","err_code":0}
    

[Delphine-L]

@Smeds @mvdbeek I'd be grateful for feedback on the latest version of the workflow.

I modified the workflow to :

1. use bwameme2 on paired collection instead of the filter and merge tool
2. take either 1 or 2 haplotypes
3. generate pretext maps with coverage and gaps even if telomeres track is empty (with all 3 tracks if not). I am not sure how often it could happen that no telomeres are detected, but it's there just in case.

Tests are :

1. one haplotype with telomeres found
2. one haplotype without telomeres found

I am not testing for 2 haplotypes right now because it takes too much memory for the CI to run, I am working on using smaller scaffolds to test it.