nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
0.9.1). 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})$Path to a fasta file of the reference sequence
stringTrim reads
booleantrueSaved failed read files after trimminng
booleanpath to file containing adapters in fasta format
string${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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanDirectory to keep pipeline Nextflow logs and reports.
string${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.
integer4Maximum amount of memory that can be requested for any single job.
string16.GB^[\d\.]+\s*.(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Parameters 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.
string