nf-core/bacass
Simple bacterial assembly and annotation pipeline
1.1.1). The latest
stable release is
2.5.0
.
Define where the pipeline should find input data and save output data.
The input design file for the pipeline.
stringThe 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})$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
stringSend plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GBMaximum amount of time that can be requested for any single job.
string240.hParameters 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 configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringPath to Kraken2 database.
stringParameters 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.
stringshortExtra arguments for Unicycler
stringThis 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.
stringSpecifies 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.
stringmedakaSkip 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