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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
39 stars 16 forks source link

added V4.1 fixes #175 #182

Closed MarieLataretu closed 2 years ago

MarieLataretu commented 2 years ago

fixes #175

I avoided a . in the folder's name, since it could have an effect, when simpleName is used.

If you prefer something else, let me know!

hoelzer commented 2 years ago

but can I already select this primer scheme now, @MarieLataretu ? via --primerV V4-1 ?

And then we should likely also add the support of this kit to the --help

hoelzer commented 2 years ago

just performing a testrun w/ this setting now (although the primer kit originally used was V4)

hoelzer commented 2 years ago

besides, run through @MarieLataretu ! nice. If the first V4.1 sequencing pops up we can try this and if it works fine merge

MarieLataretu commented 2 years ago

I updated the readme and help - also with V4 :)

nextflow run poreCov.nf -profile singularity,local,test_fastq,stub --cores 2 --max_cores 2 --primerV V4.1

works fine, but I cheated with stub.

Edit: looks also fine without stub

hoelzer commented 2 years ago

worked and looks good! amplicon recovered via V4.1 in omicron! I will merge, but once the ARTIC network puts the "offical" BED in their repository we might want to update again

thx!