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.
1.0.0). The latest
stable release is
1.1.0
.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringresultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters which enable/disable certain steps used in the workflow.
If the filtering step should be carried out.
booleanIf the pre-processed reads should be used by the filter.
booleanIf the output of kraken2 should be used for filtering.
booleanIf blastn should be skipped.
booleanSave intermediates to the results folder.
booleanParameters 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.gzSave 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.
number0.05If 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).
number0.5Ratio per read of assigned to tax2filter k-mers to unclassified k-mers.
numberThe taxon or taxonomic group to be assessed or filtered by the pipeline.
stringHomoParameters 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.
stringGRCh38Path to FASTA genome file.
stringDo not load the iGenomes reference config.
booleanbooleantrueDirectory / 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/masterInstitutional 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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
boolean