nf-core/detaxizer

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

If preprocessing with fastp should be turned on.

Signifies that bbduk is used in the classification process. Can be combined with the ‘classification_kraken2’ parameter to run both.

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.

If a validation of the classified reads via blastn should be carried out.

If the filtered reads should be classified with kraken2.

When a validation via blastn is wanted but the filtering should use the IDs from the classification process.

If the filtering step should be skipped.

Select the read-filtering tool: seqkit or bbmap. seqkit normalizes FASTQ headers by temporarily renaming them; bbmap uses filterbyname.sh for exact header matching — Note: BBTools I/O forces any base that is N to Q=0 (!).

If the removed reads should also be written to the output folder.

If the pre-processed reads should be used by the filter.

Save intermediates to the results folder.

Location of the fasta which contains the contaminant sequences.

Length of k-mers for classification carried out by bbduk

The database which is used in the classification step. Please be aware that this default database will require ~60GB download and ~80GB RAM.

Save unclassified reads and classified reads (those assigned to any taxon, not specifically assessed or filtered) to separate files. For the filtered reads.

Save unclassified reads and classified reads (those assigned to any taxon, not specifically assessed or filtered) to separate files. For the removed reads.

Confidence in the classification of a read as a certain taxon.

Confidence in the classification of a read as a certain taxon. For the filtered reads.

Confidence in the classification of a read as a certain taxon. For the removed reads.

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.

Ratio per read of assigned to tax2filter k-mers to k-mers assigned to any other taxon (except unclassified).

Ratio per read of assigned to tax2filter k-mers to unclassified k-mers.

The taxon or taxonomic group to be assessed or filtered by the pipeline.

Location of the fasta from which the blastn database will be constructed.

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.

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.

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.

fastp option defining the minimum readlength of a read

fastp option defining if the reads which failed to be trimmed should be saved

fastp option to define the threshold of quality of an individual base

fastp option to define the mean quality for trimming

fastp option if duplicates should be filtered or not before classification

fastp option to define if the clipped reads should be saved

Name of iGenomes reference.

Turn on generation of samplesheets for downstream pipelines.

Specify a comma separated string in quotes to specify which pipeline to generate a samplesheet for.

Custom MultiQC yaml file containing HTML including a methods description.