nf-core/detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
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
Parameters which enable/disable certain steps used in the workflow.
If preprocessing with fastp should be turned on.
boolean
Signifies that bbduk is used in the classification process. Can be combined with the ‘classification_kraken2’ parameter to run both.
boolean
Signifies that kraken2 is used in the classification process. Can be combined with the ‘classification_bbduk’ parameter to run both. For kraken2 alone no parameter is needed.
boolean
If a validation of the classified reads via blastn should be carried out.
boolean
If the filtered reads should be classified with kraken2.
boolean
When a validation via blastn is wanted but the filtering should use the IDs from the classification process.
boolean
If the filtering step should be carried out.
boolean
If the removed reads should also be written to the output folder.
boolean
If the pre-processed reads should be used by the filter.
boolean
Save intermediates to the results folder.
boolean
Parameter to customize bbduk execution
Location of the fasta which contains the contaminant sequences.
string
Length of k-mers for classification carried out by bbduk
integer
27
Parameters used by kraken2 to classify all reads provided. Fine-tuning of the isolation step can be done via the cutoff_*
parameters.
The database which is used in the classification step.
string
https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20240904.tar.gz
Save unclassified reads and classified reads (those assigned to any taxon, not specifically assessed or filtered) to separate files.
boolean
Save unclassified reads and classified reads (those assigned to any taxon, not specifically assessed or filtered) to separate files. For the filtered reads.
boolean
Save unclassified reads and classified reads (those assigned to any taxon, not specifically assessed or filtered) to separate files. For the removed reads.
boolean
Confidence in the classification of a read as a certain taxon.
number
Confidence in the classification of a read as a certain taxon. For the filtered reads.
number
Confidence in the classification of a read as a certain taxon. For the removed reads.
number
If a read has less k-mers assigned to the taxon/taxa to be assessed/to be filtered the read is ignored by the pipeline.
integer
Ratio per read of assigned to tax2filter k-mers to k-mers assigned to any other taxon (except unclassified).
number
Ratio per read of assigned to tax2filter k-mers to unclassified k-mers.
number
The taxon or taxonomic group to be assessed or filtered by the pipeline.
string
Homo sapiens
Parameters to fine-tune the output of blastn.
Location of the fasta from which the blastn database will be constructed.
string
Coverage is the percentage of the query sequence which can be found in the alignments of the sequence match. It can be used to fine-tune the validation step.
number
40
The expected(e)-value contains information on how many hits of the same score can be found in a database of the size used in the query by chance. The parameter can be used to fine-tune the validation step.
number
0.01
Identity is the percentage of the exact matches in the query and the sequence found in the database. The parameter can be used to fine-tune the validation step.
number
40
Options to control the behavior of fastp
fastp option defining the minimum readlength of a read
integer
fastp option defining if the reads which failed to be trimmed should be saved
boolean
fastp option to define the threshold of quality of an individual base
integer
fastp option to define the mean quality for trimming
integer
1
fastp option if duplicates should be filtered or not before classification
boolean
fastp option to define if the clipped reads should be saved
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
GRCh38
Do not load the iGenomes reference config.
boolean
boolean
true
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Options for generating input samplesheets for complementary downstream pipelines.
Turn on generation of samplesheets for downstream pipelines.
boolean
Specify a comma separated string in quotes to specify which pipeline to generate a samplesheet for.
string
taxprofiler,mag
^(taxprofiler|mag)(?:,(taxprofiler|mag)){0,1}
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/