Some of the pipelines created using the GTO tools are available here. Inside of each directory, there is available the shell script and the README.md file details what tools where used and for what.

gto_complexity_profile_regions.sh
gto_complexity_profiles.sh
gto_create_viral_dataset.sh
gto_find_motif.sh
gto_map_rearrangements.sh
gto_map_rearrangements_proteins.sh
gto_metagenomics.sh
gto_proteins_complexity_profile_regions.sh
gto_simulate_rearragements.sh
gto_merge_fasta_dbs.sh
gto_build_xs_viral_db.sh
gto_create_sars_dataset.sh
gto_sars_simulation_detection.sh
gto_download_sars2.sh
gto_find_best_sars2.sh
gto_relative_complexity_profile.sh

1. Create a directory here with the script name and inside created a README using the following template:

   Script: gto_gto_script_name.sh

   Pipeline description...

   gto_script_name.sh

   The following block of code represents the essential information for this script:

   essential pieces of code

   Tools

   The GTO tools used and their role in this pipeline are the following:

   • gto_tool_1: the importance of this tool in the pipeline.
   • gto_tool_2: the importance of this tool in the pipeline.

2. Add the script name in this file and the README at the repository root.

3. Add the script in the conda/build.sh file. This script has the following syntax:

   • cp pipelines/gto_gto_script_name/gto_gto_script_name.sh $PREFIX/bin/