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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringresultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringParameters which enable/disable certain steps used in the workflow.
If the filtering step should be carried out.
booleanIf set to True the filter is used. Otherwise only assessing is performed.
If the pre-processed reads should be used by the filter.
booleanIf set to True the the pre-proccesed reads are used for filtering. Else the raw reads are used.
If the output of kraken2 should be used for filtering.
booleanIf this is set to True the kraken2 output is used for filtering.
If blastn should be skipped.
booleanDefines if blastn should be used or not. By default blastn is used in the workflow. If also the filter is enabled the reads are filtered using the output from blastn.
Save intermediates to the results folder.
booleanSet this parameter to True if you want to publish the intermediate files to the results folder.
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.
stringhttps://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gzFor 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.
booleanConfidence in the classification of a read as a certain taxon.
number0.05Refer to https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#confidence-scoring for details.
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.
integer2Ratio per read of assigned to tax2filter k-mers to k-mers assigned to any other taxon (except unclassified).
number0.5If 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.
numberIf 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.
stringHomoIf 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.
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.
number40The 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.
number0.01Identity 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.
number40Options to control the behavior of fastp
fastp option defining the minimum readlength of a read
integerfastp option defining if the reads which failed to be trimmed should be saved
booleanfastp option to define the threshold of quality of an individual base
integerfastp option to define the mean quality for trimming
integer15fastp option to define if the clipped reads should be saved
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringGRCh38If 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.
Path to FASTA genome file.
stringThis parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleanDo 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.
booleantrueDirectory / URL base for iGenomes references.
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/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use 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.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$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.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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
booleantrueShow all params when using --help
booleanBy 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.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.