Closed replikation closed 4 years ago
lineage_report.csv
command:
for file in */*.fasta; do pangolin -t 8 $file -o ${file%.*} ; done
# in nextflow
pangolin -t ${task.cpus} ${fasta}
csv file:
taxon,lineage,SH-alrt,UFbootstrap,lineages_version,status,note
barcode12/ARTIC/medaka,B.1,100,100,2020-04-27,passed_qc,
docker:
nanozoo/pangolin:1.0.2--d4db9dd
add this https://github.com/hCoV-2019/pangolin