Usage

Input: /path/to/samples.csv provided by the user.

Output: 1) An output config file summarizing 2) the MAGs generated by MetaBAT2 and CONCOCT.

  • /path/to/work/dir/binning/final_reports/samples.csv for ingestion by the next module (ex. quality-checking)

  • /path/to/work/dir/binning/*/sample_name/, where * is either 1_metabat2 or 2_concoct, the directories containing FastAs (*.fa) of MAGs inferred by MetaBAT2 and CONCOCT respectively

Structure:

└── workflow
    ├── Snakefile
    ├── binning.py
    ├── utils.py
    └── __init__.py

  • workflow/binning.py: Click-based CLI that wraps the snakemake and unit test generation commands for clean management of parameters, resources, and environment variables.

  • workflow/Snakefile: The snakemake pipeline.

  • workflow/utils.py:

  1. Make your own samples.csv based on the template in configs/samples.csv. Sample test data can be found in .tests/unit/map_sort/data/work_dir/tmp/.

    • samples.csv requires absolute paths to Illumina reads (currently, ingest_samples in workflow/utils.py expects FastQs) and de novo assembled contigs.

  2. Update the relevant metabat2 and concoct parameters in configs/parameters.yaml.

  3. Update the computational resources available to the pipeline in resources/*.yaml where * is either ‘slurm’ or ‘bash’.

4. To run CAMP on the command line, use the following, where /path/to/work/dir is replaced with the absolute path of your chosen working directory, and /path/to/samples.csv is replaced with your copy of samples.csv.

python /path/to/camp_binning/workflow/binning.py \
    -w /path/to/camp_binning/workflow/Snakefile \
    -d /path/to/work/dir \
    -s /path/to/samples.csv

  • Note: This setup allows the main Snakefile to live outside of the work directory.

  1. To run CAMP on a job submission cluster (for now, only Slurm is supported), use the following.

    • --slurm is an optional flag that submits all rules in the Snakemake pipeline as sbatch jobs.

::

sbatch -j jobname -e jobname.err.log -o jobname.out.log << “EOF” #!/bin/bash python /path/to/camp_binning/workflow/binning.py –slurm

-w /path/to/camp_binning/workflow/Snakefile -d /path/to/work/dir -s /path/to/samples.csv

EOF