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feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. #584

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@Smeds Smeds commented Oct 28, 2024

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

@Smeds Smeds marked this pull request as draft October 28, 2024 14:03
@Smeds Smeds changed the title feat: updated version of pretext workflow developed by Delphine that … feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. Oct 28, 2024
@mvdbeek
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mvdbeek commented Oct 30, 2024

@Smeds
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Smeds commented Oct 30, 2024

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.

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

@Delphine-L Delphine-L marked this pull request as ready for review November 26, 2024 03:37
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I am not sure why the tests are not running. Could someone take a look ?

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mvdbeek commented Nov 26, 2024

Screenshot 2024-11-26 at 09 51 41

I assume that's the reason ?

Comment on lines 11 to 24
HiC reads - forward:
class: Collection
collection_type: list
elements:
- class: File
identifier: HiC forward reads
location: https://zenodo.org/records/14218240/files/Hi-C%20forward%20reads.fastqsanger.gz
HiC reads - reverse:
class: Collection
collection_type: list
elements:
- class: File
identifier: HI-C reverse reads
location: https://zenodo.org/records/14218240/files/HI-C%20reverse%20reads.fastqsanger.gz
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Why is this not a paired collection ?

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Because we are aligning the two separately as single reads to the reference. If we use a paired collection BWA-MEM2 will align them as paired reads with an expected distance between the pairs and that won't work for Hi-C

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Are you basing this pipeline on something existing ? Otherwise -SP would disable pairing and mate rescue.

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Yes, it's based on the pipeline they have been using for the VGP. It does the same separate alignment in scaffolding workflow, and it has a specific tool for merging alignments for Arima Hi-C reads. Also the workflow 4, assembly with HiC, needs them to be in 2 separate collections, so it may be easier for the user to use the same collections throughout the whole process. We can discuss using the -SP option for a future release, we'd need to test is works the same.

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Yeah, I would bring that up. What tool is this ?

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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/.

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Total 0
Passed 0
Error 0
Failure 0
Skipped 0

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3 participants