PerMedCoE Covid19 Pilot workflow (Nextflow)

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COVID-19 Multiscale Modelling of the Virus and Patients’ Tissue Workflow

Description

Uses multiscale simulations to predict patient-specific SARS‑CoV‑2 severity subtypes (moderate, severe or control), using single-cell RNA-Seq data, MaBoSS and PhysiBoSS. Boolean models are used to determine the behaviour of individual agents as a function of extracellular conditions and the concentration of different substrates, including the number of virions. Predictions of severity subtypes are based on a meta-analysis of personalised model outputs simulating cellular apoptosis regulation in epithelial cells infected by SARS‑CoV‑2.

The workflow uses the following building blocks, described in order of execution:

High-throughput mutant analysis
Single-cell processing
Personalise patient
PhysiBoSS
Analysis of all simulations

Code Snippets

"""
sed  's/\t/,/g' $meta_tsv > "meta.csv" 
"""

NextFlow From line 34 of NextFlow/covid19_pilot.nf

"""
MaBoSS_BB -d --model epithelial_cell_2 --data_folder ${params.data_dir} --parallel ${task.cpus} --ko_file ko_file.txt
"""

NextFlow MaBoSS From line 46 of NextFlow/covid19_pilot.nf

"""
mkdir result
single_cell_processing_BB -d --p_id ${p_id} --p_group ${group} --p_file ${sample_file} --parallelize ${task.cpus} --norm_data result/norm_data.tsv --raw_data result/raw_data.tsv --scaled_data result/scaled_data.tsv --cells_metadata result/cells_metadata.tsv --outdir images
"""

NextFlow From line 58 of NextFlow/covid19_pilot.nf

"""
personalize_patient_BB -d --norm_data ${res_dir}/norm_data.tsv --cells ${res_dir}/cells_metadata.tsv --model_prefix ${params.model_prefix} --t ${params.cell_type} --ko $ko --model_output_dir \$PWD/model --personalized_result personal 
"""

NextFlow From line 71 of NextFlow/covid19_pilot.nf

"""
PhysiBoSS_BB -d --sample $p_id --repetition $rep --prefix $cfg_file.baseName --bnd_file $bnd_file --cfg_file $cfg_file --parallel ${task.cpus} --max_time ${params.max_time} --out_file physiboss.out --err_file physiboss.err --results_dir \$PWD/${p_id}_${cfg_file.baseName}_physiboss_run_${rep}
"""

NextFlow PhysiBoSS From line 83 of NextFlow/covid19_pilot.nf

"""

ids=(\$(ls -1 | grep epithelial_cell_2 | cut -d '_' -f1 | sort | uniq ))
for i in "\${ids[@]}"; do
    mkdir -p \$i/physiboss_results
    mv \${i}_* \$i/physiboss_results
    rename \${i}_ "" \$i/physiboss_results/*
done

meta_analysis_BB -d --meta_file $params.meta_file --out_dir \$PWD --model_prefix ${params.model_name} --ko_file $ko --reps $params.repetitions --verbose 0 --results \$PWD/meta_res
"""