nf-core/bacass
Simple bacterial assembly and annotation pipeline
1.1.1). The latest
stable release is
2.4.0
.
Define where the pipeline should find input data and save output data.
The input design file for the pipeline.
stringUse this to specify the location of your input design file. For example:
--input 'design_hybrid.tsv'
An example of properly formatted input files can be found at the nf-core/testData. Exemplarily, this is the input used for a hybrid assembly in testing:
ID R1 R2 LongFastQ Fast5 GenomeSize
ERR044595 https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz https://github.com/nf-core/test-datasets/raw/bacass/nanopore/subset15000.fq.gz NA 2.8m
IDThe identifier to use for handling the dataset e.g. sample nameR1The forward reads in case of available short-read dataR2The reverse reads in case of available short-read dataLongFastQThe long*read FastQ file with reads in FASTQ formatFast5The folder containing the basecalled FAST5 filesGenomeSizeThe expected genome size of the assembly. Only used by the canu assembler.
Missing values (e.g. FAST5 folder in case of short reads) can be omitted by using a NA in the TSV file. The pipeline will handle such cases appropriately then.
The output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Workflow name.
stringA custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infostrings3://ngi-igenomes/igenomes/stringtrueSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GBUse to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.hUse to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringPath 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.
Parameters for the assembly
The assembler to use for assembly. Available options are Unicycler, Canu, Miniasm. The latter two are only available for long-read data, whereas Unicycler can be used for short or hybrid assembly projects.
stringunicyclerWhich type of assembly to perform.
stringshortThis adjusts the type of assembly done with the input data and can be any of long, short or hybrid. Short & Hybrid assembly will always run Unicycler, whereas long-read assembly can be configured separately using the --assembler parameter.
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.
This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.
stringThe annotation method to annotate the final assembly. Default choice is prokka, but the dfast tool is also available. For the latter, make sure to create your specific config if you're not happy with the default one provided. See #dfast_config to find out how.
stringprokkaExtra 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`
Specifies a configuration file for the DFAST annotation method. This can be used instead of PROKKA if required to specify a specific config file for annotation. If you want to know how to create your config file, please refer to the DFAST readme on how to create one. > The default config is just included for testing, so if you want to annotate using DFAST, you have to create a config!
string/Users/alexanderpeltzer/IDEA/nf-core/bacass/assets/test_config_dfast.pyWhich assembly polishing method to use.
stringmedakaCan be used to define which polishing method is used by default for long reads. Default is medaka, available options are nanopolish or medaka.
Skip running Kraken2 classifier on reads.
stringSkip annotating the assembly with Prokka /DFAST.
stringSkip running PycoQC on long read input.
stringSkip polishing the long-read assembly with FAST5 input. Will not affect short/hybrid assemblies.
string