nf-core/bacass
Simple bacterial assembly and annotation pipeline
Define where the pipeline should find input data and save output data.
Path to tab-separated sample sheet
stringThe 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})$Parameters for QC and trim short-reads
save trimmed files
booleansave files that failed to pass trimming thresholds ending in *.fail.fastq.gz
booleanSkip FastQC
booleanSkip Nanoplot
booleanSkip ToulligQC
booleanSkip FastP
booleanSpecify true to not write any reads that pass trimming thresholds.This can be used to use fastp for the output report only.
booleanTool for ONT read filtering
stringporechopArguments for running Filtlong
stringMinimun length for Filtlong to work
integer10Path to Kraken2 database.
stringPath to the Kmerfinder bacteria database (ie: ‘/path_to/kmerfinder/bacteria/ or ‘/path_to/kmerfinder/bacteria.tar.gz’). Only taxonomic group ‘bacteria’ is allowed. See database installation (guidelines)[https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/] for details. The latest version can be downloaded from the KmerFinder Database FTP site or directly during pipeline execution with. Example:
--kmerfinderdb 'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz'
(Note: Downloading the KmerFinder database (~30GB) via FTP can be time-consuming. It’s recommended to pre-download the database and provide the *.tar.gz file using this parameter instead of URL site.).
An older version is available on (Zenodo)[https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz].
stringReference FASTA file.
stringReference GFF file.
stringParameters for the assembly
The assembler to use for assembly. Use the appropriate assembler according to the chosen assembly_type. Refer to the README.md for further clarification.
stringWhich type of assembly to perform.
stringExtra arguments for Unicycler
stringAllowed technologies for long read assembly.
stringThis can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.
stringOptions for running BUSCO
BUSCO lineage to use, you can use other BUSCO lineages, these are available in: https://busco.ezlab.org/list_of_lineages.html
stringbacteria_odb10BUSCO mode to use
stringPath to BUSCO database
string,nullPath to BUSCO config file
string,nullClean intermediate BUSCO files
booleanWhich assembly polishing method to use.
stringParameters for the annotation
The annotation method to annotate the final assembly.
stringExtra arguments for prokka annotation tool.
stringFASTA file with protein sequences to be used as reference by PROKKA.
stringPath to Bakta database
stringDownload Bakta database
booleanSpecifies a configuration file for the DFAST annotation method.
stringassets/test_config_dfast.pyUse the reference files (.fasta, .gff) from kmerfinder step for LIFTOFF.
booleanSkip running Kraken2 classifier on reads.
booleanSkip annotating the assembly with Prokka /DFAST.
booleanSkip running PycoQC on long read input.
booleanSkip BUSCO
booleanSkip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies.
booleanSkip MultiQC
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.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
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.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string