Sunbeam: How to Set-up / Run

Before running sunbeam, you will need to mount the condo environment using the following command: conda activate sunbeam3.1.1

  1. Move to the directory where you plan to set up and run your analysis:
  2. sunbeam init analysis_sunbeam --data_fp /path/to/directory --force --format {sample}_R{rp}_001.fastq.gz #This will create a folder titled analysis_sunbeam and generate a config file and .csv file of the samples located in /path/to/directory

    As currently written, files in /path/to/directory need to be paired files that are in .fastq.gz format with the following suffix: {sample}_R{rp}_001.fastq.gz, where {sample} defines the sample name and {rp} defines the 1 or 2 in the read pair

  3. After building your directory, you will need to make a few edits to your config file:
  4. Open your editor for the sunbeam_config.yml file in the analysis_sunbeam folder

    Though not necessary, under the all header, edit the output_fp parameter if you want to change the name of your analysis output folder

    Under the qc header, edit the host_fp parameter to the location of the .fasta files for host/contaminant genomes - all files should be located in the same directory

    Under the classify header, edit the kraken_db_fp parameter to the path to the Kraken database that you wish to use for taxonomic assignment

  5. sunbeam run -- --configfile sunbeam_config.yml all_qc #Choose which step you need to run: all_qc can be replaced with other steps in the pipeline (e.g., all_decontam, all_assembly, all_reports)
  6. If restarting from previous step, add the following to the command: --rerun-triggers mtime --rerun-incomplete -k