nf-core/taxprofiler

Path to comma-separated file containing information about the samples and libraries/runs.

Path to comma-separated file containing information about databases and profiling parameters for each taxonomic profiler

Specify to save decompressed user-supplied TAR archives of databases

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.

Specify to skip sequencing quality control of raw sequencing reads

Specify the tool used for quality control of raw sequencing reads

Save reads from samples that went through the adapter clipping, pair-merging, and length filtering steps for both short and long reads

Save only the final reads from all read processing steps (that are sent to classification/profiling) in results directory.

Turns on short read quality control steps (adapter clipping, complexity filtering etc.)

Specify which tool to use for short-read QC

Skip adapter trimming

Specify adapter 1 nucleotide sequence

Specify adapter 2 nucleotide sequence

Specify a list of all possible adapters to trim. Overrides —shortread_qc_adapter1/2. Formats: .txt (AdapterRemoval) or .fasta. (fastp).

Turn on merging of read pairs for paired-end data

Include unmerged reads from paired-end merging in the downstream analysis

Specify the minimum length of reads to be retained

Perform deduplication of the input reads (fastp only)

Turns on nucleotide sequence complexity filtering

Specify which tool to use for complexity filtering

Specify the minimum sequence entropy level for complexity filtering

Specify the window size for BBDuk complexity filtering

Turn on masking rather than discarding of low complexity reads for BBduk

Specify the minimum complexity filter threshold of fastp

Specify the complexity filter mode for PRINSEQ++

Specify the minimum dust score for PRINTSEQ++ complexity filtering

Save reads from samples that went through the complexity filtering step

Turns on long read quality control steps (adapter clipping, length filtering etc.)

Specify which tool to use for adapter trimming.

Skip long-read trimming

Specify which tool to use for long reads filtering

Skip long-read length and quality filtering

Specify the minimum length of reads to be retained

Specify the percent of high-quality bases to be retained

Filtlong only: specify the number of high-quality bases in the library to be retained

Nanoq only: specify the minimum average read quality filter (Q)

Turn on short-read metagenome sequencing redundancy estimation with nonpareil. Warning: only use for shallow short-read sequencing datasets.

Specify mode for identifying redundant reads

Turn on short-read host removal

Turn on long-read host removal

Specify path to single reference FASTA of host(s) genome(s)

Specify path to the directory containing pre-made BowTie2 indexes of the host removal reference

Specify path to a pre-made Minimap2 index file (.mmi) of the host removal reference

Save mapping index of input reference when not already supplied by user

Saved mapped and unmapped reads in BAM format from host removal

Save reads from samples that went through the host-removal step

Turn on run merging

Save reads from samples that went through the run-merging step

Turn on profiling with Centrifuge. Requires database to be present CSV file passed to —databases

Turn on saving of Centrifuge-aligned reads

Turn on profiling with DIAMOND. For unmerged paired-read libraries, only read1 will be used Requires database to be present CSV file passed to —databases

Specify output format from DIAMOND profiling.

Turn on saving of DIAMOND-aligned reads. Will override —diamond_output_format and no taxon tables will be generated

Turn on profiling with Kaiju. Requires database to be present CSV file passed to —databases

Turn on expanding of virus hits to individual viruses rather than aggregating at a taxonomic level.

Specify taxonomic rank to be displayed in Kaiju taxon table

Turn on profiling with Kraken2. Requires database to be present CSV file passed to —databases

Turn on saving of Kraken2-aligned reads

Turn on saving of Kraken2 per-read taxonomic assignment file

Turn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.

Turn on profiling with KrakenUniq. Requires one or more KrakenUniq databases to be present in the CSV file passed to —databases.

Turn on saving of KrakenUniq (un-)classified reads as FASTA.

Specify a RAM chunk size for all KrakenUniq databases when loading into memory when you want to load via chunks. Specify in --databases for per-database values.

Turn on saving of KrakenUniq per-read taxonomic assignment file.

Specify the number of samples for each KrakenUniq run.

Turn on Bracken (and the required Kraken2 prerequisite step).

Turn on the saving of the intermediate Kraken2 files used as input to Bracken itself into Kraken2 results folder

Turn on profiling with MALT. Requires database to be present CSV file passed to —databases

Specify which MALT alignment mode to use

Turn on saving of MALT-aligned reads

Turn on generation of MEGAN summary file from MALT results

Turn on profiling with MetaPhlAn. Requires database to be present CSV file passed to —databases

Turn on saving of MetaPhlAn reads aligned against marker genes in SAM format

Turn on profiling with mOTUs. Requires database to be present CSV file passed to —databases

Turn on printing relative abundance instead of counts.

Turn on saving the mgc reads count.

Turn on removing NCBI taxonomic IDs.

Turn on classification with KMCP.

Turn on saving the output of KMCP search

Turn on profiling with ganon. Requires database to be present CSV file passed to —databases.

Turn on saving of ganon per-read taxonomic assignment file(s).

Specify the type of ganon report to save.

Specify the taxonomic report the ganon report file should display.

Specify a percentile within which hits will be reported in ganon report output..

Specify a minimum number of reads a hit must have to be retained in the ganon report.

Specify a maximum number of reads a hit must have to be retained in the ganon report.

Turn on standardisation of taxon tables across profilers

Turn on generation of BIOM output (currently only applies to mOTUs)

Turn on generation of Krona plots for supported profilers

Specify path to krona taxonomy directories (required for MALT krona plots)

The desired output format.

The path to a directory containing taxdump files.

Add the taxon name to the output. Requires —taxpasta_taxonomy_dir.

Add the taxon rank to the output. Requires —taxpasta_taxonomy_dir.

Add the taxon’s entire name lineage to the output. Requires —taxpasta_taxonomy_dir.

Add the taxon’s entire ID lineage to the output. Requires —taxpasta_taxonomy_dir.

Add the taxon’s entire rank lineage to the output. Requires —taxpasta_taxonomy_dir.

Ignore individual profiles that cause errors.

Custom MultiQC yaml file containing HTML including a methods description.