Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adding binning-only flag, simplify recipes #192

Merged
merged 20 commits into from
Mar 12, 2024
Merged
Changes from 1 commit
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
fix: parallel genomes passed to lorikeet correctly
  • Loading branch information
rhysnewell committed Mar 5, 2024
commit 2d947538d72061cbfd6c67277964f38792233634
2 changes: 1 addition & 1 deletion aviary/modules/strain_analysis/scripts/run_lorikeet.py
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def run_lorikeet(
else:
short_reads = ""

lorikeet_cmd = f"lorikeet call -t {threads} -d {mag_directory} -x {mag_extension} -p {parallel_genomes} {short_reads} {long_reads} -o {output_directory} --do-not-call-svs --calculate-dnds --calculate-fst".split()
lorikeet_cmd = f"lorikeet call -t {threads} -d {mag_directory} -x {mag_extension} -P {parallel_genomes} {short_reads} {long_reads} -o {output_directory} --do-not-call-svs --calculate-dnds --calculate-fst".split()

run(lorikeet_cmd)

Expand Down
Loading