nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
1.0.0). The latest
stable release is
1.2.3
.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples and libraries/runs.
string^\S+\.(csv)$Path to comma-separated file containing information about databases and profiling parameters for each taxonomic profiler
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringCommon options across both long and short read preprocessing QC steps
Specify the tool used for quality control of raw sequencing reads
stringSave reads from samples that went through the adapter clipping, pair-merging, and length filtering steps for both short and long reads
booleanOptions for adapter clipping, quality trimming, pair-merging, and complexity filtering
Turns on short read quality control steps (adapter clipping, complexity filtering etc.)
booleanSpecify which tool to use for short-read QC
stringSkip adapter trimming
booleanSpecify adapter 1 nucleotide sequence
stringNoneSpecify adapter 2 nucleotide sequence
stringNoneSpecify a list of all possible adapters to trim. Overrides —shortread_qc_adapter1/2. Formats: .txt (AdapterRemoval) or .fasta. (fastp).
stringNoneTurn on merging of read pairs for paired-end data
booleanInclude unmerged reads from paired-end merging in the downstream analysis
booleanSpecify the minimum length of reads to be retained
integer15Turns on nucleotide sequence complexity filtering
booleanSpecify which tool to use for complexity filtering
stringSpecify the minimum sequence entropy level for complexity filtering
number0.3Specify the window size for BBDuk complexity filtering
integer50Turn on masking rather than discarding of low complexity reads for BBduk
booleanSpecify the minimum complexity filter threshold of fastp
integer30Specify the complexity filter mode for PRINSEQ++
stringSpecify the minimum dust score for PRINTSEQ++ complexity filtering
number0.5Save reads from samples that went through the complexity filtering step
booleanOptions for adapter clipping, quality trimming, and length filtering
Turns on long read quality control steps (adapter clipping, length filtering etc.)
booleanSkip long-read trimming
booleanSkip long-read length and quality filtering
booleanSpecify the minimum length of reads to be retained
integer1000Specify the percent of high-quality bases to be retained
integer90Specify the number of high-quality bases in the library to be retained
integer500000000Options for pre-profiling host read removal
Turn on short-read host removal
booleanTurn on long-read host removal
booleanSpecify path to single reference FASTA of host(s) genome(s)
stringNoneSpecify path to the directory containing pre-made BowTie2 indexes of the host removal reference
stringNoneSpecify path to a pre-made Minimap2 index file (.mmi) of the host removal reference
stringNoneSave mapping index of input reference when not already supplied by user
booleanSaved mapped and unmapped reads in BAM format from host removal
booleanSave reads from samples that went through the host-removal step
booleanOptions for per-sample run-merging
Turn on run merging
booleanSave reads from samples that went through the run-merging step
booleanTurn on profiling with Centrifuge. Requires database to be present CSV file passed to —databases
booleanTurn on saving of Centrifuge-aligned reads
booleanTurn on profiling with DIAMOND. Requires database to be present CSV file passed to —databases
booleanSpecify output format from DIAMOND profiling.
stringTurn on saving of DIAMOND-aligned reads. Will override —diamond_output_format and no taxon tables will be generated
booleanTurn on profiling with Kaiju. Requires database to be present CSV file passed to —databases
booleanSpecify taxonomic rank to be displayed in Kaiju taxon table
stringTurn on profiling with Kraken2. Requires database to be present CSV file passed to —databases
booleanTurn on saving of Kraken2-aligned reads
booleanTurn on saving of Kraken2 per-read taxonomic assignment file
booleanTurn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.
booleanTurn on profiling with KrakenUniq. Requires database to be present CSV file passed to —databases
booleanTurn on saving of KrakenUniq-aligned reads
booleanSpecify how large to chunk database when loading into memory for KrakenUniq
string16GTurn on saving of KrakenUniq per-read taxonomic assignment file
booleanTurn on Bracken (and the required Kraken2 prerequisite step).
booleanTurn on profiling with MALT. Requires database to be present CSV file passed to —databases
booleanSpecify which MALT alignment mode to use
stringBlastNTurn on saving of MALT-aligned reads
booleanTurn on generation of MEGAN summary file from MALT results
booleanTurn on profiling with MetaPhlAn3. Requires database to be present CSV file passed to —databases
booleanTurn on profiling with mOTUs. Requires database to be present CSV file passed to —databases
booleanTurn on printing relative abundance instead of counts.
booleanTurn on saving the mgc reads count.
booleanTurn on removing NCBI taxonomic IDs.
booleanTurn on standardisation of taxon tables across profilers
booleanTurn on generation of BIOM output (currently only applies to mOTUs)
booleanTurn on generation of Krona plots for supported profilers
booleanSpecify path to krona taxonomy directories (required for MALT krona plots)
stringNoneThe desired output format.
stringThe path to a directory containing taxdump files.
stringAdd the taxon name to the output.
booleanAdd the taxon rank to the output.
booleanAdd the taxon’s entire name lineage to the output.
booleanAdd the taxon’s entire ID lineage to the output.
booleanParameters 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$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$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.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
boolean