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Authors:
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Lluis
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Paula
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Aina
Description
Snakemake
workflow to identify the best protein-protein complex obtained from different different protein docking programs (e.g., ftdock, zdock)
Repository Content
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The input_files folder contains the PDB structures of protein-protein complexes from ftdock and zdock docking programs.
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The logs folder contains the log files from the workflow.
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The results folder contains the best configuration for each docking program.
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The scripts folder contains the python scripts used in the workflow.
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Script to run the workflow.
Installation steps
- Install enviroment:
conda env create -f environment.yml
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Define all variables in
config.yaml -
Execute test workflow dryrun:
./test_rule_graph.sh
- Execute run workflow:
./run_workflow.sh
Details of the workflow
rule_graph.svg
Details of the execution in
snakemake_report.html
Code Snippets
41 42 | shell: "(python3 {input.script} {input.xtc} {input.topology} {output.pdb}) &> {log}" |
60 61 | shell: "(python3 {input.script} -i {input.pdb} -o {output.dist} -s {params.sasa} -d {params.d_cut}) &> {log}" |
81 82 | shell: "(cat {params.prefix1}* > {output.all}) &> {log}" |
101 102 | shell: "(python3 {input.script} -i {input.all} -r {input.ref} -x {params.xtc} -o {output.vote}) &> {log}" |
Support
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