nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringstringstringstringCommon options across both long and short read preprocessing QC steps
Specify to skip sequencing quality control of raw sequencing reads
booleanSpecify the tool used for quality control of raw sequencing reads
stringSave reads from samples that went through the adapter clipping, pair-merging, and length filtering steps for both short and long reads
booleanSave only the final reads from all read processing steps in results directory.
booleanOptions for adapter clipping, quality trimming and pair-merging
Turns on short read quality control steps (adapter clipping, read filtering etc.)
booleantrueSpecify which tool to use for short-read QC
stringSkip adapter trimming
booleanSpecify adapter 1 nucleotide sequence
stringSpecify adapter 2 nucleotide sequence
stringSpecify a list of all possible adapters to trim. Overrides —shortread_qc_adapter1/2. Formats: .txt (AdapterRemoval) or .fasta. (fastp).
stringTurn on merging of read pairs for paired-end data
booleanInclude unmerged reads from paired-end merging in the downstream analysis
booleanSpecify the minimum length of reads to be retained
integer50Perform deduplication of the input reads (fastp only)
booleanOptions for adapter clipping, quality trimming, and length filtering
Turns on long read quality control steps (adapter clipping, length filtering etc.)
booleantrueSpecify which tool to use for adapter trimming.
stringSkip long-read trimming
booleanSpecify which tool to use for long reads filtering
stringnanoqSkip long-read length and quality filtering
booleanSpecify the minimum length of reads to be retained
integer1000Specify the percent of high-quality bases to be retained
integer90Filtlong only: specify the number of high-quality bases in the library to be retained
integer500000000Nanoq only: specify the minimum average read quality filter (Q)
integer7Options for per-sample run-merging
Turn on run merging
booleantrueSave reads from samples that went through the run-merging step
booleantrueOptions for sub-sampling reads
Turn on sub-sampling of reads with Rasusa
booleantrueDesired coverage depth when sub-sampling
integer100Options for short-read mapping
Specify which tool to use for short-read mapping
stringOptions for long-read mapping
Specify the output format from minimap2 align
booleantrueSpecify the bam index file extension
stringbaiGenerate CIGAR
booleanWrite CIGAR with >65535 operators at the CG tag.
booleantruePath to Clair3 model
stringSequencing platform
stringontOptions for creating FASTA consensus files
Specify the coverage at which low coverage regions are masked with N
integer9Scale the coverage by a constant factor
string1Maximum non GATC bases (i.e - and N) to allow in consensus FASTA
number0.5