nf-core/genomeannotator
Pipeline for the identification of (coding) gene structures in draft genomes.
Define where the pipeline should find input data and save output data.
Path to the genome assembly.
string
^\S+\.fn?a(sta)?$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([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.
string
Path to samplesheet for RNAseq data.
string
^\S+\.csv$
Path to a fasta file with proteins
string
^\S+\.fn?a(sta)?$
Path to a fasta file with proteins
string
^\S+\.fn?a(sta)?$
Path to a fasta file with transcripts/ESTs
string
^\S+\.fn?a(sta)?$
Path to a fasta file with known repeat sequences for this organism
string
^\S+\.fn?a(sta)?$
Path to samplesheet for Reference genomes and annotations.
string
^\S+\.csv$
Options that control pipeline behavior
Chunk size for splitting the assembly.
integer
200000000
Maximum length of expected introns in bp.
integer
Minimum size of contig to consider
integer
5000
Taxonomic group to guide repeat masking.
string
A database of curated repeats in EMBL format.
string
https://www.dfam.org/releases/Dfam_3.5/families/Dfam_curatedonly.h5.gz
^\S+\.gz$
Name of a BUSCO taxonomic group to evaluate the completeness of annotated gene set(s).
string
Path to the local BUSCO data.
string
A placeholder gff file to help trigger certain processes.
string
PIPELINE_BASE/assets/empty.gff3
Options that control gene finding with AUGUSTUS
AUGUSTUS species model to use.
string
Options to pass to AUGUSTUS.
string
--alternatives-from-evidence=on --minexonintronprob=0.08 --minmeanexonintronprob=0.4 --maxtracks=3
Location of the AUGUSTUS config directory within the docker container
string
/usr/local/config
A custom config directory for AUGUSTUS
string
Custom AUGUSTUS extrinsic config file path
string
Length of annotation chunks in AUGUSTUS
integer
3000000
Enable training of a new AUGUSTUS profile.
boolean
Priority for protein-derived hints for gene building.
integer
3
Priority for targeted protein evidences
integer
5
Priority for transcript evidences
integer
4
Priority for RNAseq splice junction evidences
integer
4
Priority for RNAseq exon coverage evidences
integer
2
Priority for trans-mapped gene model evidences
integer
4
Evidence label for transcriptome data
string
E
Evidence label for protein data
string
P
Evidence label for RNAseq data
string
E
Options that control processing of protein evidences
Taxon model to use for SPALN protein alignments.
string
SPALN custom options.
string
-M
SPALN id threshold for aligning.
integer
60
Minimum size of a protein sequence to be included.
integer
35
Numbe of proteins per alignment job.
integer
200
Q value for the SPALN alignment algorithm.
integer
5
ID threshold for targeted protein alignments.
integer
90
Options that control the PASA transcriptome annotation pipeline
Number of PASA models to select for AUGUSTUS training.
integer
1000
Built-in config file for PASA.
string
PIPELINE_BASE/assets/pasa/alignAssembly.config
Options that control the EvidenceModeler pipeline
Weights file for EVM.
string
None
Number of EVM jobs per chunk.
integer
10
Options that control individual tool behavior
Activate the trinity assembly sub-pipeline
boolean
Activate the PASA sub-pipeline
boolean
Activate the EvidenceModeler sub-pipeline
boolean
Activate search for ncRNAs with RFam/infernal
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Send plain-text email instead of HTML.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean