nf-core/readsimulator
A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
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
Choose the data types that should be simulated by the pipeline.
Option to simulate amplicon sequencing reads.
boolean
Option to simulate target capture sequencing reads.
boolean
Option to simulate metagenomic sequencing reads.
boolean
Option to simulate wholegenomic sequencing reads.
boolean
Options for simulating amplicon sequencing reads.
Forward primer to use with crabs_insilicopcr.
string
GTCGGTAAAACTCGTGCCAGC
Reverse primer to use with crabs_insilicopcr.
string
CATAGTGGGGTATCTAATCCCAGTTTG
Number of reads to be simulated per amplicon.
integer
500
Length of reads to be simulated.
integer
130
Sequencing system of reads to be simulated.
string
Maximum number of errors allowed in CRABS insilicoPCR primer sequences
number
4.5
Options for simulating target capture sequencing reads.
Path to bait/probe file. Can be a fasta file or a bed file.
string
Name of supported probe. Mandatory if not using --probes
parameter.
string
Simulate ‘illumina’ or ‘pacbio’ reads.
string
Median of fragment size at shearing.
integer
500
Shape parameter of the fragment size distribution.
number
6
Median of fragment size distribution.
integer
1300
Shape parameter of the fragment size distribution.
number
6
Median of target fragment size (the fragment size of the data). If specified, will override ‘—fmedian’ and ‘—smedian’. Othersise will be estimated.
integer
Shape parameter of the effective fragment size distribution.
number
Number of fragments.
integer
500000
Illumina: read length.
integer
150
PacBio: Average (polymerase) read length.
integer
30000
Illumina: Sequencing mode.
string
Options for simulating metagenomic sequencing reads.
Abundance distribution.
string
Path to tab-separated file containing abundance distribution.
string
^\S+\.tsv$
Coverage distribution.
string
Path to tab-separated file containing coverage information.
string
^\S+\.tsv$
Format of FASTA file used to generate reads
string
Number of reads to generate.
string
1M
Can be ‘kde’, or ‘basic’.
string
Can be ‘HiSeq’, ‘NovaSeq’, or ‘MiSeq’.
string
Use this option to prevent simulating reads that have abnormal GC content.
boolean
Options for simulating wholegenome sequencing reads.
The base error rate.
number
0.02
The outer distance between the two ends.
integer
500
The standard deviation.
integer
50
The number of read pairs.
integer
1000000
The length of the first reads.
integer
70
The length of the second reads.
integer
70
The rate of mutations.
number
0.001
The fraction of indels.
number
0.15
The probability that an indel is extended.
number
0.3
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to reference FASTA file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Do not load the iGenomes reference config.
boolean
Path to text file containing accession ids (one accession per row).
string
Path to text file containing taxids (one taxid per row).
string
The NCBI taxonomic groups to download. Options include ‘all’, ‘archaea’, ‘bacteria’, ‘fungi’, ‘invertebrate’, ‘metagenomes’, ‘plant’, ‘protozoa’, ‘vertebrate_mammalian’, ‘vertebrate_other’, and ‘viral’. A comma-separated list is also valid (e.g., ‘bacteria,viral’).
string
all
The NCBI section to download. ‘refseq’ or ‘genbank’.
string
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
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|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
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
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean