search

kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
9 stars 3 forks source link

fix checking in racon script #13

Closed kapsakcj closed 4 years ago

kapsakcj commented 4 years ago

Currently the np_consensus_racon.sh script checks for the wrong file before aligning long reads to the flye assembly with minimap2.

https://github.com/lskatz/nanoporeWorkflow/blob/feb1b4a51d2f33653a8ea35cddac0d96fbc74052/scripts/np_consensus_racon.sh#L61

^$dir/minimap2 does not exist

If the workflow-after-gpu-basecalling.sh script was run a second time on a directory, then the racon/alignment.paf file was being overwritten.

kapsakcj commented 4 years ago

Done in https://github.com/lskatz/nanoporeWorkflow/commit/3659eae40a73e00c6793735963977f30bbd2e7ad