nf-core/ribomsqc
QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis
Define where the pipeline should find input data and save output data.
Path to a comma-separated file (CSV) listing samples to process. Must contain a header with two columns: 'id' (sample identifier) and 'raw_file' (full path to the corresponding RAW file). You may specify one or multiple samples for batch processing.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Directory where the pipeline will write its output. If a relative folder name is used (e.g., 'results'), it will be created in the current working directory. If an absolute path is given (e.g., '/path/to/output'), the folder will be created at that specific location.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringParameters used for chromatographic peak extraction and visualisation
Path to a tab-separated values (TSV) file describing the analytes for chromatographic peak extraction. Must include columns: short_name, long_name, mz_M0 (required), and optionally mz_M1, mz_M2, ms2_mz, and rt_teoretical (required). Only mz_M0 and rt_teoretical are mandatory. mz_M1 and mz_M2 are reserved for future support of isotopic envelope integration.
string^\S+\.tsv$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.
stringTime window (in seconds) around the theoretical retention time in which peaks will be searched. The window is defined as RT ± tolerance.
integer150Tolerance 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.
integer20MS level to extract chromatographic peaks from. Set to 1 for MS1 or 2 for MS2.
integer2Whether to plot MS1 XICs
booleanWhether to plot MS2 XICs
booleanOutput file name for the XIC PDF plot
stringxic_plot.pdfWhether to generate an additional TSV file accumulating the XIC extraction results. If set to true, the output will include a progressively updated results table based on the original input analytes TSV.
boolean