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got my multiple fastq file
bactopia --samples input.tsv -profile docker
then
bactopia summary --bactopia bactopia/ << the --bactopia flag as suggested by main program is not accurate, it throw an error asking for --bactopia-path.
bactopia summary --bactopia-path bactopia/
then I did a pangenome wf
bactopia --wf pangenome --run_name ph --bactopia bactopia -profile docker
followed by
bactopia --wf staphtyper --run_name ph --bactopia bactopia -profile docker
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Dear Rob and all
Thanks for the great effort.
I've made test for V3 and it is awesome.
I tested with 5 samples and 1 reference and the results are neat.
I used mamba to build the env.
docker as running engine, on linux fedora 38.
bactopia prepare -s "Staphylococcus aureus" -p fastq > input.tsv
got my multiple fastq file
bactopia --samples input.tsv -profile docker
then
bactopia summary --bactopia bactopia/ << the --bactopia flag as suggested by main program is not accurate, it throw an error asking for --bactopia-path.
bactopia summary --bactopia-path bactopia/
then I did a pangenome wf
bactopia --wf pangenome --run_name ph --bactopia bactopia -profile docker
followed by
bactopia --wf staphtyper --run_name ph --bactopia bactopia -profile docker
and all went great.
All all wonderful
M
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