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)?$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringPath 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.
integer200000000Maximum length of expected introns in bp.
integerMinimum size of contig to consider
integer5000Taxonomic group to guide repeat masking.
stringA database of curated repeats in EMBL format.
stringhttps://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).
stringPath to the local BUSCO data.
stringA placeholder gff file to help trigger certain processes.
stringPIPELINE_BASE/assets/empty.gff3Options that control gene finding with AUGUSTUS
AUGUSTUS species model to use.
stringOptions to pass to AUGUSTUS.
string--alternatives-from-evidence=on --minexonintronprob=0.08 --minmeanexonintronprob=0.4 --maxtracks=3Location of the AUGUSTUS config directory within the docker container
string/usr/local/configA custom config directory for AUGUSTUS
stringCustom AUGUSTUS extrinsic config file path
stringLength of annotation chunks in AUGUSTUS
integer3000000Enable training of a new AUGUSTUS profile.
booleanPriority for protein-derived hints for gene building.
integer3Priority for targeted protein evidences
integer5Priority for transcript evidences
integer4Priority for RNAseq splice junction evidences
integer4Priority for RNAseq exon coverage evidences
integer2Priority for trans-mapped gene model evidences
integer4Evidence label for transcriptome data
stringEEvidence label for protein data
stringPEvidence label for RNAseq data
stringEOptions that control processing of protein evidences
Taxon model to use for SPALN protein alignments.
stringSPALN custom options.
string-MSPALN id threshold for aligning.
integer60Minimum size of a protein sequence to be included.
integer35Numbe of proteins per alignment job.
integer200Q value for the SPALN alignment algorithm.
integer5ID threshold for targeted protein alignments.
integer90Options that control the PASA transcriptome annotation pipeline
Number of PASA models to select for AUGUSTUS training.
integer1000Built-in config file for PASA.
stringPIPELINE_BASE/assets/pasa/alignAssembly.configOptions that control the EvidenceModeler pipeline
Weights file for EVM.
stringNoneNumber of EVM jobs per chunk.
integer10Options that control individual tool behavior
Activate the trinity assembly sub-pipeline
booleanActivate the PASA sub-pipeline
booleanActivate the EvidenceModeler sub-pipeline
booleanActivate search for ncRNAs with RFam/infernal
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean