nf-core/macproqc: Output

Introduction

This document describes the output produced by the pipeline. All paths are relative to the top-level results directory set with --outdir.

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

• Spectra preparation — decompression and conversion to mzML
• Raw-data metrics — spectrum-level QC metrics from mzML (migrating)
• Peptide identification — decoy database generation and database search with Comet
• FDR filtering and protein inference — 1 % FDR filter and PIA protein groups (migrating)
• Feature finding — isotope feature detection with IDMapper (migrating)
• mzQC output — standardised QC metric export (migrating)
• Visualisation — interactive Plotly report (migrating)
• Pipeline information — reports from Nextflow itself

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Spectra preparation

Raw vendor files are decompressed (if necessary) and converted to the open mzML format. Thermo .raw files are converted using ThermoRawFileParser; Bruker .d folders are converted using tdf2mzml. Files already in mzML format are passed through after optional decompression.

Output files

• mzmls/
• *.mzML — converted mzML files. These are intermediate files used by downstream steps and are not published by default

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Raw-data metrics

TODO

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Peptide identification

Peptide spectrum matches (PSMs) are produced by searching the converted mzML files against a protein sequence database using the Comet search engine (STILL TODO).

Decoy database

Before the database search, the pipeline generates a target-decoy FASTA by appending decoy sequences (reversed by default) to the input database using the OpenMS DecoyDatabase tool. This step can be skipped with --skip_decoy_generation if the supplied FASTA already contains decoys.

The decoy database file is an intermediate used downstream for FDR estimation. It is only written to the output directory when --save_decoy_database true is set.

Output files

• decoy_database/
• *_decoy.fasta — combined target-decoy protein sequence database. Only present when --save_decoy_database true is set.

Comet search configuration

Before the database search, the pipeline generates a Comet parameter file by taking a template (either the built-in default at assets/default_configs/comet.params or a user-supplied file via --comet_config_template) and overwriting the search settings (mass tolerances, fragment ion parameters, modifications, and output format flags) with the pipeline parameter values.

The adjusted parameter file is an intermediate used by the Comet search step and is not written to the output directory.

Comet PSMs (migrating)

TODO

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Pipeline information

Output files

• pipeline_info/
• execution_report_<timestamp>.html — Nextflow execution report with run statistics and per-process resource usage.
• execution_timeline_<timestamp>.html — timeline of all process executions.
• execution_trace_<timestamp>.txt — tab-separated trace file with per-task resource metrics.
• pipeline_dag_<timestamp>.html — directed acyclic graph (DAG) of the pipeline workflow.
• nf_core_macproqc_software_versions.yml — versions of all software used in the pipeline run.

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.