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Australian-Structural-Biology-Computing/wisps: Output

Introduction

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

WISPS-specific outputs

Interaction generation

Output files
  • create/
    • interactions.fasta: generated interaction sequences used as model input.
    • interaction_mapping.tsv: mapping between interaction IDs and chain indices / chain labels.

This step expands the samplesheet inputs into pairwise interactions according to --mode and --interaction_neighbours.

MSA and model-input preparation

Output files
  • mmseqs/
    • *.a3m: MSA files produced by colabfold_search.
    • *.json: AlphaFold3 JSON input files (when AlphaFold3 is enabled).
    • *.yaml: Boltz YAML input files (when Boltz is enabled).
    • *.csv: Paired MSA in CSV format used by Boltz (when Boltz is enabled).

These files are generated once from the interaction FASTA and reused by downstream structure prediction tools.

Structure prediction results

Output files
  • run/ (outputs from both Boltz and AlphaFold3 modules)
    • Boltz:
      • boltz_results_*/predictions/*/*.cif: predicted structures.
      • boltz_results_*/predictions/*/confidence_*.json: confidence metrics.
      • boltz_results_*/predictions/*/affinity_*.json: affinity predictions (if produced).
      • boltz_results_*/predictions/*/pae_*.npz: PAE matrices.
    • AlphaFold3:
      • out/*/*_model.cif: top-ranked model structures.
      • out/*/*_confidences.json: detailed confidence output.
      • out/*/*_summary_confidences.json: summary confidence output.
  • colabfold/
    • *_relaxed_rank_001_*_model_*.pdb: relaxed top-ranked ColabFold structures.
    • *_scores_rank_001_*.json: model score summaries.

IPSAE and confidence summaries

Output files
  • ipsae/
    • data/*<digit>.txt: IPSAE per-structure analysis outputs.
    • ipsae_scores.csv: per-interaction summary table with maximum cross-group IPSAE scores by model.
    • ipsae_scores_<pair>.csv: per-chain-pair IPSAE tables across all interactions.
  • collect/
    • *_confidence_scores_full.csv: model-specific confidence summary tables used by MultiQC including a maximum cross-group chainwise ipTM score.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • WISPS-specific outputs - Interaction files, model inputs, structure predictions, and summary tables
  • Pipeline information - Report metrics generated during the workflow execution

MultiQC

Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.

Pipeline information

Output files
  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter's are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
    • Parameters used by the pipeline run: params.json.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.