nf-core/detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and 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$
You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
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})$
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config
) then you don't need to specify this on the command line for every run.
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 set to True
the filter is used. Otherwise only assessing is performed.
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
If set to True
the the pre-proccesed reads are used for filtering. Else the raw reads are used.
Save intermediates to the results folder.
boolean
Set this parameter to True
if you want to publish the intermediate files to the results folder.
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_20240605.tar.gz
For input how to use this parameter to fine-tune the step see the kraken2 section in the usage documentation
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
Refer to https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#confidence-scoring for details.
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
If the ratio of the sum of k-mers mapped to the taxon/taxa to be assessed/to be filtered to (sum(to keep)+sum(to filter/assess)) is below this threshold the read is ignored by the pipeline. Can take values between 0.0 and 1.0.
Ratio per read of assigned to tax2filter k-mers to unclassified k-mers.
number
If the ratio of the sum of k-mers mapped to the taxon/taxa to be assessed/to be filtered to (unclassified+sum(to filter/assess)) is below this threshold the read is ignored by the pipeline. Can take values between 0.0 and 1.0.
The taxon or taxonomic group to be assessed or filtered by the pipeline.
string
Homo sapiens
If a whole taxonomic group should be assessed/filtered use the highest taxonomic name in the hierarchy. E.g. if you want to assess for/filter out the whole taxonomic subtree from Mammalia onward provide this parameter with the string 'Mammalia'.
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
If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38
.
See the nf-core website docs for more details.
Do not load the iGenomes reference config.
boolean
Do not load igenomes.config
when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config
.
boolean
true
Directory / URL base for iGenomes references.
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
If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
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
Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
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
The Nextflow publishDir
option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
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
By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help
. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
boolean
By default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
boolean
Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/