parameters.md

plant-food-research-open/assemblyqc pipeline parameters

A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.

Input/output options

Parameter	Description	Type	Default	Required	Hidden
input	Input assembly sheet in CSV format	string		True
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
email	Email address for completion summary.	string

Validation options

Parameter	Description	Type	Default	Required	Hidden
check_sequence_duplicates	Check for duplicate sequences in fasta validation	boolean	True

General stats options

Parameter	Description	Type	Default	Required	Hidden
assemblathon_stats_n_limit	The number of 'N's for the unknown gap size. NCBI recommendation is 100	integer	100
gfastats_skip	Skip Gfastats	boolean	True

NCBI FCS options

Parameter	Description	Type	Default	Required	Hidden
ncbi_fcs_adaptor_skip	Skip NCBI FCS Adaptor checking	boolean	True
ncbi_fcs_adaptor_empire	Empire for NCBI FCS Adaptor checking: 'euk' for eukaryotes, or 'prok' for prokaryotes	string
ncbi_fcs_gx_skip	Skip NCBI FCS external organism contamination checking	boolean	True
ncbi_fcs_gx_tax_id	Tax ID for NCBI FCS GX. See: https://www.ncbi.nlm.nih.gov/taxonomy	number
ncbi_fcs_gx_db_path	Path to NCBI FCS GX database. See: https://github.com/ncbi/fcs/wiki/FCS-GX	string
contamination_stops_pipeline	Skip remaining QC steps for an assembly which has adaptor or GX contamination	boolean	True

tidk options

Parameter	Description	Type	Default	Required	Hidden
tidk_skip	Skip telomere identification	boolean	True
tidk_repeat_seq	Telomere repeat sequence. Typical values for plant: TTTAGGG, fungus, vertebrates: TTAGGG and Insect: TTAGG	string
tidk_filter_by_size	Filter assembly sequences smaller than the specified length	boolean
tidk_filter_size_bp	Filter size in base-pairs	integer	1000000

BUSCO options

Parameter	Description	Type	Default	Required	Hidden
busco_skip	Skip BUSCO	boolean	True
busco_mode	BUSCO mode: 'genome', 'transcriptome', 'proteins'	string
busco_lineage_datasets	BUSCO lineages. It should be provided as a space-separated list of lineages: 'fungi_odb10 microsporidia_odb10'	string
busco_download_path	Download path for BUSCO	string

LAI options

Parameter	Description	Type	Default	Required	Hidden
lai_skip	Skip LAI estimation	boolean	True

Kraken 2 options

Parameter	Description	Type	Default	Required	Hidden
kraken2_skip	Skip Kraken2	boolean	True
kraken2_db_path	Kraken2 database path	string

HiC options

Parameter	Description	Type	Default	Required	Hidden
hic	HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz'	string
hic_skip_fastp	Skip HiC read trimming	boolean
hic_skip_fastqc	Skip HiC read QC	boolean
hic_fastp_ext_args	Additional parameters for fastp trimming	string	--qualified_quality_phred 20 --length_required 50
hic_samtools_ext_args	Additional parameters for samtools view command run after samblaster	string	-F 3852

Merqury options

Parameter	Description	Type	Default	Required	Hidden
merqury_skip	Skip merqury analysis	boolean	True
merqury_kmer_length	kmer length for merqury analysis	integer	21

Synteny options

Parameter	Description	Type	Default	Required	Hidden
synteny_skip	Skip synteny analysis	boolean	True
synteny_mummer_skip	Skip Mummer-based synteny analysis	boolean	True
synteny_plotsr_skip	Skip plotsr-based synteny analysis	boolean	True
synteny_xref_assemblies	Reference assemblies for synteny analysis	string
synteny_between_input_assemblies	Create syntenic plots between each pair of input assemblies	boolean	True
synteny_mummer_plot_type	Synteny plot type from Mummer alignments: 'dotplot', 'circos', or 'both'	string	both
synteny_mummer_m2m_align	Include Mummer alignment blocks with many-to-many mappings	boolean
synteny_mummer_max_gap	Mummer alignments within this distance are bundled together	integer	1000000
synteny_mummer_min_bundle_size	After bundling, any Mummer alignment bundle smaller than this size is filtered out	integer	1000000
synteny_plot_1_vs_all	Create a separate synteny plot for each contig of the target assembly versus all contigs of the reference assembly. This only applies to Mummer plots	boolean
synteny_color_by_contig	Mummer synteny plots are colored by contig. Otherwise, they are colored by bundle size	boolean	True
synteny_plotsr_seq_label	Sequence label prefix for plotsr synteny	string	Chr
synteny_plotsr_assembly_order	The order in which the assemblies should be compared, provided as space separated string of assembly tags. If absent, assemblies are ordered by their tags alphabetically.	string

OrthoFinder options

Parameter	Description	Type	Default	Required	Hidden
orthofinder_skip	Skip orthofinder	boolean	True

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	master		True
custom_config_base	Base directory for Institutional configs.	string	https://raw.githubusercontent.com/nf-core/configs/master		True
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Description	Type	Default	Required	Hidden
version	Display version and exit.	boolean			True
publish_dir_mode	Method used to save pipeline results to output directory.	string	copy		True
email_on_fail	Email address for completion summary, only when pipeline fails.	string			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
monochrome_logs	Do not use coloured log outputs.	boolean			True
hook_url	Incoming hook URL for messaging service	string			True