Support single-end (SE) reads

[tseemann]

Should Shovill support SE reads?

[rpetit3]

I'm thinking about implementing this. What are your thoughts (preference) on a separate command (shovill-se?) for only SE reads, or adding the "PE or SE" logic to shovill?

Con for the separation approach is reflecting changes across both. Pro would be not affecting shovill, so it keeps working.

Con for single file is multiple PE or SE checks may litter the main shovill. Pro is its all in one place.

[rpetit3]

For the time being, I created an alternate shovill-se (https://github.com/rpetit3/shovill/blob/single-end-reads/bin/shovill-se) based on v1.0.4 (3fe8e19)

I've omitted the steps that were for paired reads only. Its available at my personal anaconda acount: https://anaconda.org/rpetit3/shovill and installable with conda via conda install -c rpetit3 shovill

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Update: use Bioconda

conda create -n shovill-se -c conda-forge -c bioconda shovill-se 

[lskatz]

Correction: Installable with conda install -c rpetit3 shovill-se

Thank you for making this @rpetit3 !

[rpetit3]

No problem, I'd recommend to use the one from Bioconda instead of my personal channel

https://bioconda.github.io/recipes/shovill-se/README.html