In Step 1c (Data processing), there is code to move the all.uniq.tab and all.uniq.fasta files from results/id_data into results/bad_controls_path. This didn't work for me (Molly running on 3/17/25) until I added in full end-to-end pathways for the files.
Original code:
move_files(c(here("results/id_data", "all.uniq.fasta"), here("results/id_data", "all.uniq.tab")), here("results/bad_controls_path"), overwrite = FALSE)
Molly's edited code:
move_files(c(here("/oscar/data/tkartzin/mtest/obitools2-preprocessing-pipeline/20250313T14:20:30Z/2025-02-12/results/id_data", "all.uniq.fasta"), here("/oscar/data/tkartzin/mtest/obitools2-preprocessing-pipeline/20250313T14:20:30Z/2025-02-12/results/id_data", "all.uniq.tab")), here("/oscar/data/tkartzin/mtest/obitools2-preprocessing-pipeline/20250313T14:20:30Z/2025-02-12/results/bad_controls_path"), overwrite = FALSE)
In Step 1c (Data processing), there is code to move the all.uniq.tab and all.uniq.fasta files from results/id_data into results/bad_controls_path. This didn't work for me (Molly running on 3/17/25) until I added in full end-to-end pathways for the files.
Original code:
move_files(c(here("results/id_data", "all.uniq.fasta"), here("results/id_data", "all.uniq.tab")), here("results/bad_controls_path"), overwrite = FALSE)
Molly's edited code:
move_files(c(here("/oscar/data/tkartzin/mtest/obitools2-preprocessing-pipeline/20250313T14:20:30Z/2025-02-12/results/id_data", "all.uniq.fasta"), here("/oscar/data/tkartzin/mtest/obitools2-preprocessing-pipeline/20250313T14:20:30Z/2025-02-12/results/id_data", "all.uniq.tab")), here("/oscar/data/tkartzin/mtest/obitools2-preprocessing-pipeline/20250313T14:20:30Z/2025-02-12/results/bad_controls_path"), overwrite = FALSE)