cli.md

Genomeannotator command line options

input_output_options Input/output options

--assembly [ string ]

Path to the genome assembly.

--outdir [ string ]

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

--email [ string ]

Email address for completion summary.

--multiqc_title [ string ]

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

--rnaseq_samples [ string ]

Path to samplesheet for RNAseq data.

--proteins [ string ]

Path to a fasta file with proteins

--proteins_targeted [ string ]

Path to a fasta file with proteins

--transcripts [ string ]

Path to a fasta file with transcripts/ESTs

--rm_lib [ string ]

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

--references [ string ]

Path to samplesheet for Reference genomes and annotations.

annotation_module_options Options for pipeline behavior

--npart_size [ integer ]

Chunk size for splitting the assembly.

--max_intron_size [ integer ]

Maximum length of expected introns in bp.

--min_contig_size [ integer ]

Minimum size of contig to consider

--rm_species [ string ]

Taxonomic group to guide repeat masking.

--rm_db [ string ]

A database of curated repeats in EMBL format.

--busco_lineage [ string ]

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

--busco_db_path [ string ]

Path to the local BUSCO data.

--eggnog_mapper_db [ string ]

Path to a pre-installed EggnogMapper database.

--eggnog_taxonomy [ integer ]

Taxonomy ID for EggnogMapper

--dummy_gff [ string ]

A placeholder gff file to help trigger certain processes.

augustus_options Options for ab-initio gene finding

--aug_species [ string ]

AUGUSTUS species model to use.

--aug_options [ string ]

Options to pass to AUGUSTUS.

--aug_config_dir [ string ]

A config directory for AUGUSTUS

--aug_extrinsic_cfg [ string ]

Custom AUGUSTUS extrinsic config file path

--aug_chunk_length [ integer ]

Length of annotation chunks in AUGUSTUS

--aug_training [ boolean ]

Enable training of a new AUGUSTUS profile.

--pri_prot [ integer ]

Priority for protein-derived hints for gene building.

--pri_prot_target [ integer ]

Priority for targeted protein evidences

--pri_est [ integer ]

Priority for transcript evidences

--pri_rnaseq [ integer ]

Priority for RNAseq splice junction evidences

--pri_wiggle [ integer ]

Priority for RNAseq exon coverage evidences

--pri_trans [ integer ]

Priority for trans-mapped gene model evidences

--t_est [ string ]

Evidence label for transcriptome data

--t_prot [ string ]

Evidence label for protein data

--t_rnaseq [ string ]

Evidence label for RNAseq data

protein_tool_options Options for protein data processing

--spaln_taxon [ string ]

Taxon model to use for SPALN protein alignments.

--spaln_options [ string ]

SPALN custom options.

--spaln_protein_id [ integer ]

SPALN id threshold for aligning.

--min_prot_length [ integer ]

Minimum size of a protein sequence to be included.

--nproteins [ integer ]

Numbe of proteins per alignment job.

--spaln_q [ integer ]

Q value for the SPALN alignment algorithm.

--spaln_protein_id_targeted [ integer ]

ID threshold for targeted protein alignments.

pasa_options Options for PASA behavior

--pasa_nmodels [ integer ]

Number of PASA models to select for AUGUSTUS training.

--pasa_config_file [ string ]

Built-in config file for PASA.

--pasa_aligner [ string ]

Aligners to use in PASA pipeline.

evm_options Options for EvidenceModeler behavior

--evm_weights [ string ]

Weights file for EVM.

--nevm [ integer ]

Number of EVM jobs per chunk.

--evm_segment_size [ integer ]

The segment size to use in EVM in bp.

--evm_overlap_size [ integer ]

The overlap size to use in EVM in bp.

annotation_tool_options Options for tool behavior

--trinity [ boolean ]

Activate the trinity assembly sub-pipeline

--pasa [ boolean ]

Activate the PASA sub-pipeline

--evm [ boolean ]

Activate the EvidenceModeler sub-pipeline

--ncrna [ boolean ]

Activate search for ncRNAs with RFam/infernal

institutional_config_options Institutional config options

--custom_config_version [ string ]

Git commit id for Institutional configs.

--custom_config_base [ string ]

Base directory for Institutional configs.

--config_profile_name [ string ]

Institutional config name.

--config_profile_description [ string ]

Institutional config description.

--config_profile_contact [ string ]

Institutional config contact information.

--config_profile_url [ string ]

Institutional config URL link.

max_job_request_options Max job request options

--max_cpus [ integer ]

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

--max_memory [ string ]

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

--max_time [ string ]

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

generic_options Generic options

--help [ boolean ]

Display help text.

--version [ boolean ]

Display version and exit.

--publish_dir_mode [ string ]

Method used to save pipeline results to output directory.

--email_on_fail [ string ]

Email address for completion summary, only when pipeline fails.

--plaintext_email [ boolean ]

Send plain-text email instead of HTML.

--max_multiqc_email_size [ string ]

File size limit when attaching MultiQC reports to summary emails.

--monochrome_logs [ boolean ]

Do not use coloured log outputs.

--hook_url [ string ]

Incoming hook URL for messaging service

--multiqc_config [ string ]

Custom config file to supply to MultiQC.

--multiqc_logo [ string ]

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

--multiqc_methods_description [ string ]

Custom MultiQC yaml file containing HTML including a methods description.

--tracedir [ string ]

Directory to keep pipeline Nextflow logs and reports.

--validate_params [ boolean ]

Boolean whether to validate parameters against the schema at runtime

--show_hidden_params [ boolean ]

Show all params when using --help