nf-core/ribomsqc

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Introduction

nf-core/ribomsqc is a quality control (QC) pipeline designed for monitoring mass spectrometry performance in ribonucleoside analysis. It parses RAW files, performs XIC extraction using analyte definitions, and generates summary plots with MultiQC.

Samplesheet input

Before running the pipeline, you must provide a samplesheet CSV file containing metadata about the RAW files to be processed. The pipeline supports one or multiple samples, each defined on a separate line in the CSV.

--input '[path to samplesheet.csv]'

The samplesheet must contain a header and two columns:

id,raw_file
Day_5,/full/path/to/Day_5.raw
Sample_XYZ,/another/path/to/Sample_XYZ.raw

Column descriptions

• id: Unique identifier for the sample. This can be any descriptive label and is used to name output files.
• raw_file: Full path to the corresponding RAW instrument file. Multiple entries can be included to analyze several samples in one pipeline run.

Analytes TSV input

To define which compounds should be targeted for chromatographic extraction (XIC), the pipeline requires a tab-delimited TSV file passed with:

--analytes_tsv '[path to analytes.tsv]'

This file must follow a strict format and include the following columns in this exact order:

Column Descriptions

Column Descriptions

Notes

• The retention times in rt_teoretical must reflect your instrument’s chromatography performance.
• If multiple transitions are known, you can fill in mz_M1, mz_M2, and ms2_mz for more targeted detection.
• At least one compound must be selected at runtime using the --analyte parameter.

Output directory (--outdir)

The --outdir parameter specifies where the pipeline output files will be stored. Its behavior depends on how the path is defined:

• If a relative folder name is provided (e.g., results), the directory will be created in the current working directory from which the pipeline is launched.
• If an absolute path is given (e.g., /home/user/project/ribomsqc_output), the output will be created exactly at the specified location.

Running the pipeline

Typical command:

nextflow run nf-core/ribomsqc \
  --input /home/proteomics/mydata/csv/samplesheet.csv \
  --analytes_tsv /home/proteomics/mydata/tsv/qcn1.tsv \
  --analyte m3C \
  --rt_tolerance 150 \
  --mz_tolerance 20 \
  --ms_level 2 \
  --plot_xic_ms1 false \
  --plot_xic_ms2 false \
  --plot_output_path xic_plot \
  --overwrite_tsv true \
  --outdir results \
  -profile singularity

Alternatively, you can define parameters in a separate file:

Minimal params.yaml example

input: /home/proteomics/mydata/csv/samplesheet.csv
analytes_tsv: /home/proteomics/mydata/tsv/qcn1.tsv
analyte: m3C
rt_tolerance: 150
mz_tolerance: 20
ms_level: 2
plot_xic_ms1: false
plot_xic_ms2: false
plot_xic_ms2: false
plot_output_path: xic_plot
overwrite_tsv: true
outdir: results

Run with:

nextflow run nf-core/ribomsqc -profile singularity -params-file params.yaml

MultiQC Integration

The pipeline integrates MultiQC. It collects the consolidated .json files generated by the MERGEJSONS module to summarise QC metrics. Output is stored in ${params.outdir}.

Reproducibility

Use -r to specify a pipeline version:

nextflow run nf-core/ribomsqc -r 1.0.1dev ...

Update the pipeline:

nextflow pull nf-core/ribomsqc

Core Nextflow options

• -profile docker|singularity|conda|podman|...: Choose execution environment
• -resume: Resume from a previous run
• -params-file: Load parameters from a YAML/JSON file
• -c: Load additional config for cluster resources, etc.

Tips

• Use -profile singularity for reproducibility
• Compatible with Wave containers for dynamic container resolution
• For cluster configs, see nf-core/configs

Example output

results/
├── thermorawfileparser/
│   └── *.mzML
├── msnbasexic/
│   └── *.json
├── mergejsons/
│   └── *_merged_mqc.json
├── multiqc/
│   └── multiqc_report.html
└── pipeline_info/
    └── nf_core_ribomsqc_software_versions.yml

Generated with ❤️ by nf-core and adapted for custom analyte QC workflows.