nf-core/plasmodiumdrugres
Pipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. It translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.
Define where the pipeline should find input data and save output data.
Path to json file containing metadata and microhaplotypes according to pmo format.
string^\S+\.json$Path to tab separated file containing microhaplotypes for specimens.
string^\S+\.[ct]sv$Path to input samplesheet (unused; kept for nf-core template lint compatibility).
nullPath to BED file containing individual loci of interest.
string^\S+\.bed$Path to tab separated file containing groups of loci of interest. Multi-locus allele frequency estimation is skipped when this parameter is not provided.
string,null^\S+\.[ct]sv$Path to BED file containing panel location information.
string^\S+\.bed$Path to tab separated file containing population assignment for each specimen_name.
string^\S+\.[ct]sv$Comma-separated list of PMO specimen metadata field names to combine into the population label (e.g. “collection_country, collection_date”). Whitespace is ignored.
string,nullString used to join the selected pmo_population_fields when building the population label.
string,null_The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringoutputEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Reference genome related files and options required for the workflow.
Path to FASTA file containing the full genome.
string^\S+\.fn?a(sta)?(\.gz)?$Path to FASTA file containing the reference for only the targets.
string^\S+\.fn?a(sta)?(\.gz)?$Parameters used to define the methods used for each step of the pipeline.
Method for multi-locus allele frequency estimates.
stringMethod for single-locus allele frequency estimates.
stringExtra arguments supplied when translating loci of interest
stringNaive SLAF method when –slaf_method is naive.
stringlabel for population/ this individual pipeline run.
stringpop1when running MLBM, a cut off value for filtering amino acid calls.
integer,nullNaive MLAF method when –mlaf_method is naive.
stringwsaf cut off for naive multilocus estimates.
number,nullCOI lrank for dcifer slaf wrapper.
integer,nullqstart for dcifer slaf wrapper.
number,nulltolerance for dcifer slaf wrapper.
number,nullTool used for –slaf_method mhaps_freq.
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanBoolean 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/refs/heads/plasmodiumdrugres/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
boolean