feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input. #584
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…takes HiFi and HiC as input.
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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. |
... and modify the replacement expressions so that users don't have to add the &. to the suffixes
… go around the fasta implicit conversion problem
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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 |
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I am not sure why the tests are not running. Could someone take a look ? |
workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga
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I assume that's the reason ? |
| 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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workflows/VGP-assembly-v2/Pre-Curation_PretextMap/PretextMap_Generation.ga
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workflows/VGP-assembly-v2/Pre-Curation_PretextMap/.dockstore.yml
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workflows/VGP-assembly-v2/Pre-curation-Hi-C-map-generation/PretextMap_Generation-tests.yml
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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/.
updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input.