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In order to run this pipeline I have followed the instructions as in this github page. I have `miniconda3` installed and I have installed `snakemake` with `conda install -c bioconda -c conda-forge sna…
BCArg updated
4 years ago
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Is there a parameter option that will allow MAPS not to do read deduplication? Or is there a script I can edit in the package that will allow me to skip the deduplication process? Can you point me in …
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### Description of the bug
There are a couple of things to address before a first release:
- [x] Move all containers to be biocontainers
- [ ] Migrate the code to follow guidelines on nf-core:
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Following our discussion with @nekrut , I am creating an issue to outline essential components for creating a barebones HIV (or other short RNA virus) genomic analysis pipeline.
Key steps for ampl…
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### What happened?
[reporter's note: IIRC, exit code 137 indicates that the "container" in which the worker JVM was executing exceeded memory limits. It seems likely that whole stage codegen has eith…
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"RTQC methods" and "RTQC methods doi" are currently mandatory in the global attribute and in the variable attribute.
I suggest we remove it from the global attribute and leave it mandatory in the var…
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(I would like to benchmark)
Streaming into trimmomatic should be fairly easy with named pipes using wget from ENA.
Streaming from trimmomatic into broken-paired format (for e.g. diginorm) will requi…
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The current advice from ONT regarding how to perform duplex basecalling is here:
https://community.nanoporetech.com/posts/guppy-v6-0-0-release (dated 6th December 2021 - login required to view)
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### Contact Details
_No response_
### Description of changes
[workbook-3.xlsx](https://github.com/ranchobiosciences/Data_Modeling_Issues_Templates/files/10725594/workbook-3.xlsx)
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Since the pipeline version started running, all values have become `True`. Are the units with `False` values being filtered out?