nf-core/genomeqc
Compare the quality of multiple genomes, along with their annotations.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringA string with NCBI taxonomic groups of the assemblies. Can be a comma-separated list.
stringallA flag to set the busco mode for genome and annotation mode (‘genome’ is hardcoded in genome only mode).
stringA flag to set the busco lineage.
stringhymenoptera_odb10A flag to set the BUSCO lineages directory (optional)
stringA path to a BUSCO config file (optional)
stringRemove intermediate files
booleanMinimum number of Complete BUSCOs a sequence must have to be counted as significant ortholog-containing sequences.
integerPath to FCS-GX contamination screening database.
stringPath to FCS GX contamination screening database
stringRun genomeqc on genomes only.
booleank-mer size for meryl (merqury).
integer21Do not run TIDK.
booleanPublish sorted fasta genome files from seqkit.
booleanPublish gff files validated by AGAT.
booleanPublish genomes and/or annotations of user-supplied RefSeq IDs.
booleanPublish extracted protein fasta files by GFFREAD.
booleanPublish orthofinder results.
booleanPublish longest protein isoform fasta files.
booleanPublish filtered fasta genome files from seqkit.
booleanSkip these stat plots in the genome and annotation tree plot.
stringnseqs_plotSkip these stat plots in the genome only tree plot.
stringnseqs_plotTool for gxf validation.
stringModifies scale of the tree plot in the tree summary, default value is ‘0.0005’. Useful if tree tips overlap with the concatenated plots. Very sensitive, increase/decrease by two-fold.
integerstring