A launcher tool for sorting a sequencing run by pathogen and automatic initialization of their downstream pipelines. Build for routine NGS at ProvLab.
When PipelineWorksheet.xlsx is filled in, launch with:
conda activate ngs-pipeline-launcher
move_sequencing_files </path/to/src/> </path/to/dest/>
run_pipeline_launcher </path/to/run/> [E-mail]Conda is required to build the environment with the necessary workflow dependencies. To create the environment and setup the run command:
conda env create -f ./environments/environment.yml -y
conda activate ngs-pipeline-launcher
cd $CONDA_PREFIX
mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d
touch ./etc/conda/activate.d/env_vars.sh
touch ./etc/conda/deactivate.d/env_vars.sh
printf '#!/bin/sh\nrun_pipeline_launcher() { bash /path/to/pipelineLauncher.sh $1 $2; }\nexport -f run_pipeline_launcher\nmove_sequencing_files() { python /path/to/moveToAPLGenomics.py --p $1 --d $2; }\nexport -f move_sequencing_files' >> ./etc/conda/activate.d/env_vars.sh
printf '#!/bin/sh\nunset run_pipeline_launcher\unset move_sequencing_files' >> ./etc/conda/deactivate.d/env_vars.shThis file species the run information in [Header], the output directories in [Directories], the pipelines to use in [Pipelines], and the sample information in [Samples].
The output files are determined by the particular pipelines being run, and will be located in the folders specified by [Directories] in the PipelineWorksheet.xlsx
Please see \Laboratory Documents\Cross-Site\Research\Starting Pathogen Analysis via the Pipeline Launcher on Paradigm