To run the AMR pipeline on test samples, we used the runner script run-select-final.sh to call sub-scripts to run each tool (main-amr, main-species, kma-amr, kma-species)
The script was run as follows:
bash run-select-final.sh INPUT_R1.fastq INPUT_R2.fastq INPUT_contigs.fasta
Here is a specific example:
bash run-select-final.sh amr-experiment-mrsa-files/RR108e_00071_S1_207817_reads_nh_R1.fastq.gz amr-experiment-mrsa-files/RR108e_00071_S1_207817_reads_nh_R2.fastq.gz amr-experiment-mrsa-files/RR108e_00071_S1_207817_contigs_nh.fasta
The final results were combined be merging the *-amr and *-species results for each of main and kma, and then finally merging the main and kma outputs into a combined result table. This was done using the jupyter notebook preview_results_per_sample.ipynb. The output was a .tsv file.
The combined results were then parsed into final small and large table formats to be used in UXR testing (or otherwise ingested into the web app). This was done using the notebook configure_results.ipynb. There was some additional manual formatting done to generate the final UXR samples.