nf-core/bacass
Simple bacterial assembly and annotation pipeline
2.0.0
). The latest
stable release is
2.4.0
.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string
^\S+\.csv$
Path to the output directory where the results will be saved.
string
./results
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Path to Kraken2 database.
string
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.
string
unicycler
Which type of assembly to perform.
string
short
Extra arguments for Unicycler
string
This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.
string
Which assembly polishing method to use.
string
medaka
The 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.
string
prokka
Extra arguments for prokka annotation tool.
string
Specifies a configuration file for the DFAST annotation method.
string
assets/test_config_dfast.py
Skip running Kraken2 classifier on reads.
boolean
Skip annotating the assembly with Prokka /DFAST.
boolean
Skip running PycoQC
on long read input.
boolean
Skip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional configs hostname.
string
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Method used to save pipeline results to output directory.
string
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean
Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
boolean