nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
v0.9). The latest
stable release is
1.0.0
.
Define where the pipeline should find input data and save output data.
Path to a sample sheet describing paths to input fastq files
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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Path to a fasta file of the reference sequence
stringTrim reads
booleantrueSaved failed read files after trimminng
booleanpath to file containing adapters in fasta format
string${baseDir}/assets/adapters.fasTurn off subsampling
booleanDesired coverage depth when subsampling
integer100Specify genome size for subsampling rather than estimation using mash sketch
stringRemove recombination using gubbins
booleanMaximum non GATC bases (i.e - and N) to allow in pseudogenome sequences
number0.5Build a tree using the RapidNJ neighbour-joining algorithm
booleanBuild a tree using the FastTree approximate ML algorithm
booleanBuild a tree using the IQ-TREE ML algorithm
booleanBuild a tree using the RAxML-NG ML algorithm
booleanLess 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.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Directory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
booleanNOT USED: File size limit when attaching MultiQC reports to summary emails.
string25.MBNOT USED: Skip MultiQC
booleanCustom config file to supply to MultiQC.
stringCustom title for the MultiQC report.
stringenable conda rather than use containers
booleanBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer4Use 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.
string16.GB^[\d\.]+\s*.(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Use 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.
string