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.
stringGeneral options that control which parts of the pipeline run.
Run genomeqc on genomes only.
booleank-mer size for meryl (merqury).
integer21Container engine to run shiny app
stringdockerOptions for BUSCO completeness assessment.
A string with NCBI taxonomic groups of the assemblies. Can be a comma-separated list.
stringallA 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.
integerSkip BUSCO. If run on genome only, it will also skip orthofinder.
booleanOptions for FCS-GX/FCS-adaptor contamination screening.
Path to FCS-GX contamination screening database.
stringPath to FCS GX contamination screening database
stringPath to RAM-backed tmpfs or ramfs location to store FCS-GX database
stringSave cleaned genome after decontamination with FCS-GX
booleanSave cleaned genome after adaptor removal with FCS-GX
booleanOptions for annotation (GFF/GTF) validation.
Tool for gxf validation.
stringOptions for orthology inference.
OrthoFinder major version to run.
stringPublish orthofinder results.
booleantruePublish longest protein isoform fasta files.
booleanOptions for telomere identification with TIDK.
Do not run TIDK.
booleanDNA string for tidk motif search
stringOptions for the summary tree plot.
Modifies 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.
integerTree’s right margin size for the non-circular layouts.
stringTree layout style for the tree summary plot.
stringCircular layout only: which summary stats to draw as rings.
stringCircular layout only: phylogenetic-group thresholds used to score the quality (traffic-light) rings.
stringCircular layout only: override individual –quality_preset cut-offs.
stringCircular layout only: print each value on its ring.
booleanSkip these stat plots in the genome and annotation tree plot.
stringnseqs_plotSkip these stat plots in the genome only tree plot.
stringnseqs_plotOptions to publish intermediate files that are not saved by default.
Publish 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 filtered fasta genome files from seqkit.
booleanOptions for transposable element annotation.
TE annotation method to run. Use ‘hite’ for HiTE or ‘repeatmasker’ for the full RepeatMasker pipeline. Omit to skip TE annotation.
stringSet to true for plant genomes (passed to HiTE).
booleanPath to a curated repeat library for HiTE.
stringPath to pre-staged famdb h5 partition file(s). Accepts a single file path or a glob pattern (e.g. ‘/path/FamDB*’). Alternative to downloading via RM_db.
stringTaxonomic lineage to filter repeat families from famdb (e.g. ‘hymenoptera’). Omit to export all families.
stringRun de novo repeat discovery with RepeatModeler before masking. Disabled by default — RepeatModeler typically requires 24 CPUs and 24–48 h per genome. When false, only the curated famdb library is used.
booleanRepeatMasker sensitivity/speed mode. ‘default’ is most sensitive; ‘q’ (quick) is ~5x faster; ‘qq’ (rush) is fastest with lowest sensitivity.
stringDownload h5 partition files from the URLs specified in RM_db.
booleanList of URLs to DFAM h5 partition files to download.
arrayClustering tool used to dereplicate the repeat library before RepeatMasker. ‘mmseqs’ uses MMseqs2 easy-cluster; ‘linclust’ (default) uses MMseqs2 easy-linclust (linear time, less sensitive); ‘cdhit’ uses CD-HIT-EST.
stringMinimum sequence identity threshold (0.0–1.0) for repeat library clustering. Passed as -c to CD-HIT-EST and –min-seq-id to MMseqs2.
number0.8Minimum alignment coverage threshold (0.0–1.0) for repeat library clustering. Passed as -aS to CD-HIT-EST and -c (with –cov-mode 1) to MMseqs2.
number0.8Parameters 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/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.
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