Closed kapsakcj closed 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
$dir/minimap2
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.
workflow-after-gpu-basecalling.sh
racon/alignment.paf
Done in https://github.com/lskatz/nanoporeWorkflow/commit/3659eae40a73e00c6793735963977f30bbd2e7ad
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 existIf the
workflow-after-gpu-basecalling.sh
script was run a second time on a directory, then theracon/alignment.paf
file was being overwritten.