A set of python, perl and bash scripts for generating PDF reports (of C. difficile samples) produced from the outputs of Bugflow DSL2 pipeline
The script batch_process_cdiff.sh will generate all the individual sample reports. It does this by gathering the various outputs from bugflow, notably the mlst, amr/toxin profile, kraken2/bracken, cgmlst. The cgmlst is used to find related samples in the batch which is shown at the end of the report.
A python script is also run to summarise the outputs from everything into a wide summary csv.
Then to create the group report we form a list of all the consensus fastas. We then cluster into groups based on cgmlst distance. For each group we use the RunListCompare process to create a phylogeny which is ten visualised with ggtree. Finally the group report is created giving qc pass/fail for each sample, and the cluster trees below.
- Python >= 3.8
Clone the repository:
git clone https://github.com/oxfordmmm/cdiff_reporting
First-time users:
cd cdiff_reporting/
python -m venv venv
source venv/bin/activate
pip install -r requirements.txt
When the virtual environmet has been populated before:
source venv/bin/activate
You'll also need to make an environment for run list compare. The environment file is bin/clustering_rlc/rlc_env.yaml
Alternatively a conda environment can be created from environment.yml
bash batch_process_cdiff.sh -s /path/to/Bugflow/output/directory/ -d ~/data \
-c /path/to/Bugflow/output/directory/cgmlst \
-o /path/to/Bugflow/output/directory/report
See example_run.sh for a full example of running the BugFlow workflows and all the steps to generate all the reports.