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: asembler_ont and assembler_hifi.
stringWhen strategy is ‘scaffold’, which assembly should be scaffolded onto which?
stringExpected genome size, optional.
stringFlye assembly 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.
booleanAdapters for ONT read-trimming.
stringAdditional args to be passed to fastplong for ONT reads.
stringPath to HiFi reads.
stringAdapters 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
String describing the polishing strategy. Takes priority over boolean selectors. If missing will be created from boolean selectors.
stringPolish 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).
booleanAligner to use for HiC reads; default: 'bwa-mem2'.
stringOptions for QC tools
Run merqury if short reads are provided.
booleanLong 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 data-base (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 provide 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).
booleanOptions 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.
booleanOptions for HiC short reads
Trim HiC short reads.
booleanPath to forward HiC short reads.
stringPath to reverse HiC short reads.
string