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I have created and tested two separated pipelines for each Docker file but I would like to join them in one.
For that I create a single pipeline and two services: scipion-worker and scipion-master.
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Right now we don't have a way of including field maps in our [QC pipeline](https://github.com/TIGRLab/datman/blob/master/bin/qc.py). Is there something we could/should be doing with these field maps t…
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This will be the first step of the pipeline.
Implement the following software into a Snakemake pipeline to QC nanopore data
- [x] https://github.com/wdecoster/NanoPlot
- [ ] https://github.com/Genom…
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### Feature Request
This issue is a solicitation for feedback on an idea.
I've been working on the [RSV pipeline](https://github.com/CDPHE-bioinformatics/CDPHE-RSV) and reusing tasks from this r…
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## Is your feature request related to a problem? Please describe
I think it would be good to have [SoupX](https://github.com/constantAmateur/SoupX) or a similar tool as part of the pipeline.
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Hi,
I'm just wanting to check in regarding how to obtain an all-sites VCF using snpArcher. From what I can tell, I just need to add the -all-sites flag to the GenotypeGVCFs command in the following…
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# Independent user test of GATK-SV single-sample pipeline on Biowulf
Ben previously configured the GATK-SV single-sample pipeline for Biowulf and tested using a COVNET WGS sample. I ran an independ…
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MSID: 96085
Version: 2
Preprint DOI: https://doi.org/10.1101/2024.02.15.24302255
## Step 1. Awaiting reviews
**Editorial to post reviews via hypothesis**
**Useful links:**
- DocMap: https://data-…
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- [ ] Add post process in the pipeline to change the range in date type annotations.
- [ ] Add QC to verify all annotations related to date use xsd:dateTime range
> I tried changing the datatype t…
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This has been unnecessary for awhile now by the addition of pending results data to the XML files, but now that we've converted over to a pure Python pipeline, it's probably time to do away with this …