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.
string
Email 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.
string
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
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 config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
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
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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.
string
string
string
string
Common options across both long and short read preprocessing QC steps
Specify to skip sequencing quality control of raw sequencing reads
boolean
Specify the tool used for quality control of raw sequencing reads
string
Save reads from samples that went through the adapter clipping, pair-merging, and length filtering steps for both short and long reads
boolean
Save only the final reads from all read processing steps in results directory.
boolean
Options for adapter clipping, quality trimming and pair-merging
Turns on short read quality control steps (adapter clipping, read filtering etc.)
boolean
true
Specify which tool to use for short-read QC
string
Skip adapter trimming
boolean
Specify adapter 1 nucleotide sequence
string
Specify adapter 2 nucleotide sequence
string
Specify a list of all possible adapters to trim. Overrides —shortread_qc_adapter1/2. Formats: .txt (AdapterRemoval) or .fasta. (fastp).
string
Turn on merging of read pairs for paired-end data
boolean
Include unmerged reads from paired-end merging in the downstream analysis
boolean
Specify the minimum length of reads to be retained
integer
50
Perform deduplication of the input reads (fastp only)
boolean
Options for adapter clipping, quality trimming, and length filtering
Turns on long read quality control steps (adapter clipping, length filtering etc.)
boolean
true
Specify which tool to use for adapter trimming.
string
Skip long-read trimming
boolean
Specify which tool to use for long reads filtering
string
nanoq
Skip long-read length and quality filtering
boolean
Specify the minimum length of reads to be retained
integer
1000
Specify the percent of high-quality bases to be retained
integer
90
Filtlong only: specify the number of high-quality bases in the library to be retained
integer
500000000
Nanoq only: specify the minimum average read quality filter (Q)
integer
7
Options for per-sample run-merging
Turn on run merging
boolean
true
Save reads from samples that went through the run-merging step
boolean
true
Options for sub-sampling reads
Turn on sub-sampling of reads with Rasusa
boolean
true
Desired coverage depth when sub-sampling
integer
100
Options for short-read mapping
Specify which tool to use for short-read mapping
string
Options for long-read mapping
Specify the output format from minimap2 align
boolean
true
Specify the bam index file extension
string
bai
Generate CIGAR
boolean
Write CIGAR with >65535 operators at the CG tag.
boolean
true
Path to Clair3 model
string
Sequencing platform
string
ont
Options for creating FASTA consensus files
Specify the coverage at which low coverage regions are masked with N
integer
9
Scale the coverage by a constant factor
string
1
Maximum non GATC bases (i.e - and N) to allow in consensus FASTA
number
0.5