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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
tags One or more comma separated tags for nf-shard 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 (accepted: euk|prok) 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 (accepted: 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 True
hic_fastp_ext_args Additional parameters for fastp trimming string --qualified_quality_phred 20 --length_required 50
hic_save_trimmed To save or not to save the trimmed FastQ files boolean
hic_map_combinations Space separated tags, e.g. "tag1 tag2:tag3". In "tag2:tag3", "tag2" is the query in refsort. null implies separate map for each input assembly. string
hic_alphanumeric_sort Sort FASTA sequences by their labels for creating the HiC contact map? boolean True
hic_refsort Apply HapHic refsort to query fasta in paired HiC map combinations boolean True
hic_mapq HiC MAPQ threshold to apply at the YAHS juicer pre stage integer 1
hic_assembly_mode To set or not to set the assembly mode for YAHS juicer pre stage boolean True

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 (accepted: both|dotplot|circos) 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 of comparison 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

Mapback profile options

Parameter Description Type Default Required Hidden
mapback_skip Skip creation of Mapback profiles boolean True
mapback_variants_skip Skip the variants track when creating the mapback profile boolean True
mapback_clair3_platform Platform for Clair3 model selection (accepted: hifi|ont) string
mapback_coverage_span_bp Span in bp for T2T-Polish/pafToCovClippedWig tool integer 1024
mapback_gc_het_window_bp Window length in bp for summarising % GC content, 0/1 GT count and mean allele balance integer 10000
mapback_rolling_median_bp Length in bp for the rolling median filter applied to Mapback stats for plotting integer 100000

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. (accepted: symlink|rellink|link|copy|copyNoFollow|move) 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
trace_report_suffix Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss. string True