nf-core/funcprofiler
Read-based functional profiling of microbiome sequencing data
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$Path to comma-separated file containing information about databases and profiling parameters for each taxonomic profiler
string^\S+\.csv$Specify to save decompressed user-supplied TAR archives of databases
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSkip quality control step when preprocessing
booleanOptions for per-sample run-merging
Turn on run merging
booleantrueSave reads from samples that went through the run-merging step
booleanTurn on profiling with fmhfunprofiler; Requires database to be present CSV file passed to —databases
booleanTurn on profiling with HUMAnN3. Requires humann_v3-tagged database to be present CSV file passed to —databases
booleanTurn on profiling with HUMAnN4. Requires humann_v4-tagged database to be present CSV file passed to —databases
booleanTurn on translated alignment with DIAMOND blastx. Requires a .dmnd database to be present in the CSV file passed to —databases
booleansave copies-per-million outputs from HUMAaN
booleanTurn on profiling with RGI. Requires database to be present CSV file passed to —databases
booleanTurn on profiling with mi-faser. Requires database to be present CSV file passed to —databases
booleanTurn on functional annotation with EggNOG-mapper. Requires eggnogmapper-tagged database entries in the CSV file passed to —databases
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean 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/funcprofiler/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string