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kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
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add support for NB13-24 workflow-after-gpu-basecalling.sh #24

Closed kapsakcj closed 3 years ago

kapsakcj commented 4 years ago

fix the for loop.

kapsakcj commented 4 years ago

Should be able to do something like this:

$ seq -w 1 24
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kapsakcj commented 4 years ago

or just a wildcard for barcodeDir in demux/barcode*/; do [...]

kapsakcj commented 3 years ago

kit that Justin request support for: EXP-NBD114

I already have support in some local commits, but have not pushed them to master branch yet.

in workflows/workflow-after-gpu-basecalling.sh the loop has been adjusted:

-for barcodeDir in ${OUTDIR}demux/barcode[0-12]*; do
+for barcodeDir in ${OUTDIR}demux/barcode{01..24}; do

need to make sure that Guppy commands use the config for the exp-nbd114 kit

and update guppy to latest version available via scicomp modules

kapsakcj commented 3 years ago

Implemented in https://github.com/kapsakcj/nanoporeWorkflow/commit/01103076d82b2af315759fb87bdd0f9fe815874f

Need to double-check that Guppy params for barcode kit are correct before I close this issue