parameters.md

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 | | | |

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