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
stringPath to sample sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml), that points to compressed fastq files.
The sample sheet must have six tab-separated columns/entries with the following headers:
ID(required): Unique sample IDs, must start with a letter, and can only contain letters, numbers or underscoresR1(optional): Paths to (forward) reads zipped FastQ filesR2(optional): Paths to reverse reads zipped FastQ files, required if the data is paired-endLongFastQ(optional): Paths to long reads zipped FastQ filesFast5(optional): Paths to the directory containing FAST5 filesGenomeSize(optional): A number (including decimals) ending with 'm', representing genome size.
Please be aware that files will be required based on the chosen assembly type specified with the '--assembly_type' option, which can be set to one of the following values: ['short', 'long', 'hybrid'].`
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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
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
booleanTool for ONT read filtering
stringporechopArguments for running Filtlong
stringMinimun length for Filtlong to work
integer10Path to Kraken2 database.
stringSee Kraken2 homepage for download links. Minikraken2 8GB is a reasonable choice, since we run Kraken here mainly just to check for sample purity.
Path 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:
--kmerfinder_db '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.
stringMaster file (*.txt) containing a summary of assemblies available in GeneBank or RefSeq. See: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt
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.
stringThis adjusts the type of assembly done with the input data and can be any of long, short or hybrid.
Extra arguments for Unicycler
stringThis advanced option allows you to pass extra arguments to Unicycler (e.g. "--mode conservative" or "--no_correct"). For this to work you need to quote the arguments and add at least one space.
Allowed 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.
stringExtra arguments for Dragonflye
stringThis advanced option allows you to add extra arguments to Dragonflye (e.g.: "--gsize 2.4m"). For those arguments with no values/options associated (e.g.: "--nopolish" or "--nofilter"...) you need to add an extra space at the begining of the input string to params.dragonflye_args. Example: --params.dragonflye_args ' --nopolish'
Options 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.
stringCan be used to define which polishing method is used by default for long reads.
Parameters for the annotation
The annotation method to annotate the final assembly.
stringExtra arguments for prokka annotation tool.
stringThis advanced option allows you to pass extra arguments to Prokka (e.g. " --rfam" or " --genus name"). For this to work you need to quote the arguments and add at least one space between the arguments. Example:
--prokka_args `--rfam --genus Escherichia Coli`
FASTA file with protein sequences to be used as reference by PROKKA.
stringIf a file with protein sequences are provided, PROKKA will use this to annotate proteins in the assembly.
Path to Bakta database
stringDownload Bakta database
booleanSpecifies a configuration file for the DFAST annotation method.
stringassets/test_config_dfast.pyIf you want to know how to create your config file, please refer to the DFAST readme on how to create one. The default config (assets/test_config_dfast.py) is just included for testing, so if you want to annotate using DFAST, you have to create a config!
Use 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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional 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.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
MultiQC 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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