Define where the pipeline should find input data and save output data.

Path to the genome assembly.

required
type: string
pattern: ^\S+\.fn?a(sta)?$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Path to samplesheet for RNAseq data.

type: string
pattern: ^\S+\.csv$

Path to a fasta file with proteins

type: string
pattern: ^\S+\.fn?a(sta)?$

Path to a fasta file with proteins

type: string
pattern: ^\S+\.fn?a(sta)?$

Path to a fasta file with transcripts/ESTs

type: string
pattern: ^\S+\.fn?a(sta)?$

Path to a fasta file with known repeat sequences for this organism

type: string
pattern: ^\S+\.fn?a(sta)?$

Path to samplesheet for Reference genomes and annotations.

type: string
pattern: ^\S+\.csv$

Options that control pipeline behavior

Chunk size for splitting the assembly.

type: integer
default: 200000000

Maximum length of expected introns in bp.

type: integer

Minimum size of contig to consider

type: integer
default: 5000

Taxonomic group to guide repeat masking.

type: string

A database of curated repeats in EMBL format.

type: string
default: https://www.dfam.org/releases/Dfam_3.5/families/Dfam_curatedonly.h5.gz
pattern: ^\S+\.gz$

Name of a BUSCO taxonomic group to evaluate the completeness of annotated gene set(s).

type: string

Path to the local BUSCO data.

type: string

A placeholder gff file to help trigger certain processes.

type: string
default: PIPELINE_BASE/assets/empty.gff3

Options that control gene finding with AUGUSTUS

AUGUSTUS species model to use.

type: string

Options to pass to AUGUSTUS.

type: string
default: --alternatives-from-evidence=on --minexonintronprob=0.08 --minmeanexonintronprob=0.4 --maxtracks=3

Location of the AUGUSTUS config directory within the docker container

type: string
default: /usr/local/config

A custom config directory for AUGUSTUS

type: string

Custom AUGUSTUS extrinsic config file path

type: string

Length of annotation chunks in AUGUSTUS

type: integer
default: 3000000

Enable training of a new AUGUSTUS profile.

type: boolean

Priority for protein-derived hints for gene building.

type: integer
default: 3

Priority for targeted protein evidences

type: integer
default: 5

Priority for transcript evidences

type: integer
default: 4

Priority for RNAseq splice junction evidences

type: integer
default: 4

Priority for RNAseq exon coverage evidences

type: integer
default: 2

Priority for trans-mapped gene model evidences

type: integer
default: 4

Evidence label for transcriptome data

type: string
default: E

Evidence label for protein data

type: string
default: P

Evidence label for RNAseq data

type: string
default: E

Options that control processing of protein evidences

Taxon model to use for SPALN protein alignments.

type: string

SPALN custom options.

type: string
default: -M

SPALN id threshold for aligning.

type: integer
default: 60

Minimum size of a protein sequence to be included.

type: integer
default: 35

Numbe of proteins per alignment job.

type: integer
default: 200

Q value for the SPALN alignment algorithm.

type: integer
default: 5

ID threshold for targeted protein alignments.

type: integer
default: 90

Options that control the PASA transcriptome annotation pipeline

Number of PASA models to select for AUGUSTUS training.

type: integer
default: 1000

Built-in config file for PASA.

type: string
default: PIPELINE_BASE/assets/pasa/alignAssembly.config

Options that control the EvidenceModeler pipeline

Weights file for EVM.

type: string
default: None

Number of EVM jobs per chunk.

type: integer
default: 10

Options that control individual tool behavior

Activate the trinity assembly sub-pipeline

type: boolean

Activate the PASA sub-pipeline

type: boolean

Activate the EvidenceModeler sub-pipeline

type: boolean

Activate search for ncRNAs with RFam/infernal

type: boolean

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

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

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

Display help text.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean