Nextflow Registry | nf-core/ribomsqc

nf-core/ribomsqc

QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis

Version: 1.0.0 Git revision: 1.0.0 Commit: Content hash:

Run:

Repository: nf-core/ribomsqc

Workflow: main.nf

Website: https://nf-co.re/ribomsqc

Introduction

Use nf-core/ribomsqc to:

Perform automated quality control of ribonucleoside analysis by mass spectrometry.
Summarize and visualize QC metrics through integrated MultiQC reports.

ribomsqc workflow Figure 1: General workflow overview showing the pipeline steps from RAW file input through ThermoRawFileParser conversion, MSNBase XIC extraction, JSON merging, to final MultiQC report generation.

ribomsqc workflow Figure 2: Detailed workflow diagram illustrating the data flow and process connections in the ribomsqc pipeline.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

Prepare a samplesheet with your input data, for example:
```
id,raw_file
Day_5,path/to/Day_5.raw
```

For more information, see the usage docs on required samplesheet.csv columns.

Prepare an analytes TSV file (e.g. qcn1.tsv) with your compounds and theoretical retention times. The TSV must have exactly these columns and format:

short_name	long_name	mz_M0	mz_M1	mz_M2	ms2_mz	rt_teoretical
C	Cytidine 50 μg/mL	244.0928			112.0505	555
U	Uridine 25 μg/mL	245.0768			113.0346	1566
m3C	3-Methylcytidine methosulfate 100 μg/mL	258.1084			126.0662	508
m5C	5-Methylcytidine 100 μg/mL	258.1084			126.0662	655
Cm	2-O-Methylcytidine 20 μg/mL	258.1084			112.0505	883
m5U	5-Methyluridine 50 μg/mL	259.0925			127.0502	1866
I	Inosine 25 μg/mL	269.088			137.0458	1741
m1A	1-Methyladenosine 25 μg/mL	282.1197			150.0774	523
G	Guanosine 25 μg/mL	284.0989			152.0567	1726
m7G	7-Methylguanosine 25 μg/mL	298.1146			166.0723	554

Note

Replace only the values in the rt_teoretical column with your own retention times (in seconds) for each compound.

Run the pipeline:

nextflow run nf-core/ribomsqc \
  --input samplesheet.csv \
  --analytes_tsv qcn1.tsv \
  --analyte all \
  --rt_tolerance 120 \
  --mz_tolerance 7 \
  --ms_level 1 \
  --outdir results \
  -profile singularity

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option.

For more information, see the usage docs and parameters.

Pipeline output

See results page for example output and output docs.

Credits

nf-core/ribomsqc was originally written by Roger Olivella.

Contributions and Support

For help, visit Slack #ribomsqc or see contributing guide.

Citations

See CITATIONS.md for tool references.

Ewels PA et al. (2020) The nf-core framework. Nat Biotechnol. doi:10.1038/s41587-020-0439-x

XIC extraction and plotting#

Parameters used for chromatographic peak extraction and visualisation

--analyte# required

Short name of the analyte to be extracted, as defined in the 'short_name' column of the TSV file. Use a specific value such as 'm3C' to process one analyte, or use 'all' to process all analytes defined in the TSV file.

type string

--ms_level# required

MS level to extract chromatographic peaks from. Set to 1 for MS1 or 2 for MS2.

type integer

default 2

--test_mode#

Enable test mode - pipeline continues even if analytes are not found in the data. Useful for CI testing with minimal datasets.

type boolean

default false

--analytes_tsv# required

Path to a tab-separated values (TSV) file describing the analytes for chromatographic peak extraction. Must include columns: short_name, long_name, mz_M0 (required), and optionally mz_M1, mz_M2, ms2_mz, and rt_teoretical (required). Only mz_M0 and rt_teoretical are mandatory. mz_M1 and mz_M2 are reserved for future support of isotopic envelope integration.

type string

pattern ^\S+\.tsv$

--mz_tolerance# required

Tolerance in parts-per-million (ppm) around the specified precursor m/z value (mz_M0) for XIC extraction. The window is defined as mz_M0 ± tolerance.

type integer

default 20

--plot_xic_ms1#

Whether to plot MS1 XICs

type boolean

--plot_xic_ms2#

Whether to plot MS2 XICs

type boolean

--rt_tolerance# required

Time window (in seconds) around the theoretical retention time in which peaks will be searched. The window is defined as RT ± tolerance.

type integer

default 150

--overwrite_tsv#