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plant-food-research-open/genepal pipeline parameters

A Nextflow pipeline for consensus, phased and pan-genome annotation.

Input/output options

Parameter Description Type Default Required Hidden
input Target assemblies listed in a CSV sheet string True
protein_evidence Protein evidence provided as a fasta file or multiple fasta files listed in a plain txt file string True
eggnogmapper_db_dir Eggnogmapper database directory string
eggnogmapper_tax_scope Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1 integer 1
rna_evidence FASTQ/BAM samples listed in a CSV sheet string
liftoff_annotations Reference annotations listed in a CSV sheet string
orthofinder_annotations Additional annotations for orthology listed in a CSV sheet string
outdir The output directory where the results will be saved string True
email Email address for completion summary. string True

Repeat annotation options

Parameter Description Type Default Required Hidden
repeat_annotator 'edta' or 'repeatmodeler' string repeatmodeler
save_annotated_te_lib Save annotated TE library or not? boolean
edta_is_sensitive Use '--sensitive 1' flag with EDTA or not? boolean
repeatmasker_save_outputs Save the repeat-masked genome or not? boolean

RNASeq pre-processing options

Parameter Description Type Default Required Hidden
fastqc_skip Skip FASTQC or not? boolean True
fastp_skip Skip trimming by FASTQP or not? boolean
min_trimmed_reads Exclude a sample if its reads after trimming are below this number integer 10000
fastp_extra_args Extra FASTP arguments string
save_trimmed Save FASTQ files after trimming or not? boolean
remove_ribo_rna Remove Ribosomal RNA or not? boolean
save_non_ribo_reads Save FASTQ files after Ribosomal RNA removal or not? boolean
ribo_database_manifest Ribosomal RNA fastas listed in a text sheet string ${projectDir}/assets/rrna-db-defaults.txt

RNASeq alignment options

Parameter Description Type Default Required Hidden
star_max_intron_length Maximum intron length for STAR alignment integer 16000
star_align_extra_args EXTRA arguments for STAR string
star_save_outputs Save BAM files from STAR or not? boolean
save_cat_bam SAVE a concatenated BAM file per assembly or not? boolean

Annotation options

Parameter Description Type Default Required Hidden
braker_extra_args Extra arguments for BRAKER string
liftoff_coverage Liftoff coverage parameter number 0.9
liftoff_identity Liftoff identity parameter number 0.9
eggnogmapper_evalue Only report alignments below or equal the e-value threshold number 1e-05
eggnogmapper_pident Only report alignments above or equal to the given percentage of identity (0-100) integer 35

Post-annotation filtering options

Parameter Description Type Default Required Hidden
allow_isoforms Allow multiple isoforms for gene models boolean True
enforce_full_intron_support Require every model to have external evidence for all its introns boolean True
filter_liftoff_by_hints Use BRAKER hints to filter Liftoff models boolean True
eggnogmapper_purge_nohits Purge transcripts which do not have a hit against eggnog boolean
filter_genes_by_aa_length Filter genes with open reading frames shorter than the specified number of amino acids excluding the stop codon. If set to null, this filter step is skipped. integer 24

Annotation output options

Parameter Description Type Default Required Hidden
braker_save_outputs Save BRAKER files boolean
add_attrs_to_proteins_cds_fastas Add gff attributes to proteins/cDNA/CDS fasta boolean

Evaluation options

Parameter Description Type Default Required Hidden
busco_skip Skip evaluation by BUSCO boolean
busco_lineage_datasets BUSCO lineages as a space-separated list: 'fungi_odb10 microsporidia_odb10' string eukaryota_odb10

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
max_multiqc_email_size File size limit when attaching MultiQC reports to summary emails. string 25.MB True
monochrome_logs Do not use coloured log outputs. boolean True
hook_url Incoming hook URL for messaging service string True