nf-core/taxmarker
Identify taxonomically mislabelled sequences
Define where the pipeline should find input data and save output data.
Path to a taxonomy file. If omitted, taxonomy is derived from –sequences record headers instead.
string^\S+\.(tax)|(tsv)Path to a sequences file, aligned or not, in phylip (.phy), Clustal (.aln) or fasta format (.fa, .fasta, .mfa, .alnfaa or .alnfna).
string^\S+\.(aln)|(phy)|(alnf[na]a)|(mfa)|(f[na]a)|(fa)|(fasta)$Path to an HMM profile database, used to align –sequences via hmmalign if it turns out to be unaligned. Only required when the input is unaligned.
stringName of the specific profile to use from –hmm, if that database holds more than one (e.g. Barrnap’s databases hold one profile per rRNA gene).
stringSkip the raxtax prefilter and run every sequence straight through the full EPA-ng-based placement pipeline.
booleanTaxonomic rank at which raxtax’s self-classification must agree with the declared taxonomy, counted from the most specific rank (1) upward. A sequence disagreeing at this one rank is flagged as a mislabel and skips EPA-ng placement.
integer1For already-aligned input: skip filtering out sequences with too high a proportion of alignment gaps, and run every sequence straight through the rest of the pipeline.
booleanFor already-aligned input: minimum proportion of non-gap columns a sequence must have in the alignment to be kept. Sequences below this are too short/incomplete to place reliably, and are reported separately instead of being placed.
number0.3For hmmalign-derived input: skip filtering out sequences that cover too little of the HMM profile, and run every sequence straight through the rest of the pipeline.
booleanFor hmmalign-derived input: minimum proportion of the HMM profile’s match-state columns a sequence must cover to be kept. Sequences below this are too short/incomplete to place reliably, and are reported separately instead of being placed.
number0.8Skip the phylogenetic placement subworkflow (reference tree, leave-one-out placement, scoring) entirely.
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
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})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanCustom 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/erikrikarddaniel/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.
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