nf-core/genomeassembler
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters 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/genomeassembler/Display the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
booleanOptions controlling pipeline behavior
Path to reference genome seqeunce (fasta)
stringPath to reference genome annotations (gff)
stringuse reference genome
booleanOptions controlling assembly
Assembly strategy to use. Valid choices are 'single', 'hybrid' and 'scaffold'
stringsingleAssembler to use. Valid choices depend on strategy; for single either flye or hifiasm, hybrid can be done with hifiasm and for scaffolded assembly provide the names of the assemblers separated with an underscore. The first assembler will be used for ONT reads, the second for HiFi reads. (see below, asembler1 and assembler_hifi)
stringWhen strategy is “scaffold”, which assembly should be scaffolded onto which?
stringexpected genome size, optional
stringflye mode
stringadditional args for flye
stringExtra arguments passed to hifiasm
stringassembler_ont assembles ONT reads. This option is mainly useful when building more complex samplesheets
stringArguments to be passed to assembler_ont (ONT)
stringassembler_hifi assembles HiFi reads. This option is mainly useful when building more complex samplesheets
stringArguments to be passed to assembler_hifi (HiFi)
stringPath to ONT reads
stringCollect ONT reads from several files?
booleanAdaptors for ONT read-trimming
stringAdditional args to be passed to fastplong for ONT reads
stringPath to HiFi reads
stringAdaptors for HiFi read-trimming
stringAdditional args to be passed to fastplong for HiFi reads
stringRun jellyfish and genomescope (recommended)
booleanValue of k used during k-mer analysis with jellyfish
integer21Initial hash size used by jellyfish count
string200MPolishing options
Polish assembly with pilon? Requires short reads
booleanPolish assembly with dorado (ONT only)
booleanPolish assembly with medaka (ONT only)
booleanmodel to use with medaka
stringScaffolding options
Scaffold with longstitch?
booleanScaffolding with links?
booleanScaffold with ragtag (requires reference)?
booleanScaffold using HiC reads using yahs (requires reads)?
booleantrueAligner to use for HiC reads; default: bwa-mem2
stringOptions for QC tools
Run merqury (if short reads are provided)
booleantrueLong reads that should be used for QC when both ONT and HiFi reads are provided. Options are 'ont' or 'hifi'
stringRun BUSCO?
booleanPath to busco db (optional)
stringBusco lineage to use
stringauto_eukRun quast
booleanA mapping (bam) of reads mapped to the reference can be provided for QC. If provided, alignment to reference fasta will not run.
stringCan be used to proved existing assembly will skip assembly and perform downstream steps including qc
stringA mapping (bam) of reads mapped to the provided assembly can be specified for QC. If provided, alignment to the provided assembly fasta will not run
stringIndex size to use for csi index (default: 14), creating and index of size 2^csi_index_size. See samtools index documentation for details.
integer14Options controlling annotation liftover
Lift-over annotations (requires ref_gff)?
booleantrueOptions for short reads
Use short reads?
booleanTrim short reads?
booleankmer length for meryl / merqury
integer21Path to forward short reads
stringPath to reverse short reads
stringAre shortreads paired?
stringOptions for HiC short reads
Trim HiC short reads?
booleantruePath to forward HiC short reads
stringPath to reverse HiC short reads
string