Complete Parameter Reference

Every single parameter in the entire pipeline is described here. If you need to tweak every little detail of how your samples are analyzed, you’ve come to the right place! Note that every parameter is described here, even those that shouldn’t be used, so proceed with caution!

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Description	Type	Default	Required
input	Path the folder containing input reads. Help For Illumina (paired-end) reads, the file names must be identical until the ending underscore with a read number, e.g. ‘sample1_S10_L001_R1_001.fastq.gz’ and ‘sample1_S10_L001_R2_001.fastq.gz’. The read number must be designated using either ‘_1’ and ‘_2’ or ‘_R1’ and ‘_R2’. For Nanopore reads, each fastq file is assumed to be a unique sample, so, e.g. ‘FAP01234_pass_barcode05_abcd01234_0.fastq.gz’ and ‘FAP01234_pass_barcode05_abcd01234_1.fastq.gz’ are assumed to be different samples even though they are from the same barcode. All read files must be gzipped, and have the extension ‘.fastq.gz’ or ‘.fq.gz’.	string	.
platform	NGS platform used to sequence the samples	string
paired	Flag to indicate whether the reads files are paired-end or not	boolean
interleaved	Whether paired-end reads interleaved into a single fastq file	boolean
outdir	Path to the output directory where the results will be saved.	string	./results
publish_dir_mode	How to create results files	string	copy
tracedir	Directory to keep pipeline Nextflow logs and reports.	string	${params.outdir}/pipeline_info
help	Display help text.	boolean
show_hidden_params	Show all params when using --help	boolean
custom_config_version	Git commit id for Institutional configs.	string	master
custom_config_base	Base directory for Institutional configs.	string	https://raw.githubusercontent.com/nf-core/configs/master

Kraken2 Options

Control how Kraken2 filters out host reads

Parameter	Description	Type	Default	Required
kraken2_db	Path to a Kraken2 database Help The path to a Kraken2 database that will be used to filter out host reads in the pipeline. This path will be automatically mounted into the container environments if a containerized profile is used.

Corresponds to the –db option of Kraken2.| string | None | |

BLAST options

Control what reads BLAST examines

Parameter	Description	Type	Default	Required
blast_db	Path to a folder containing a BLAST nt database	string	None
blast_target	Taxonomic IDs to keep and analyze Help A space-separated list (use quotes on the command line), of the taxonomic ids to keep based on Kraken2’s classification.

Defaults to keeping all unclassified reads and all viral reads. Note that this requires the host to be present in the Kraken2 database. When dealing with animals and the databases available from kraken2-build, this is not the case, and this parameter should be modified.| string | 0 10239 | |

Read trimming options

Options for how strictly to quality control NGS reads

Parameter	Description	Type	Default	Required
trim_minlen	Minimum length of reads Help Corresponds to the MINLEN
option of Trimmomatic for Illumina reads.

Corresponds to the –length option of NanoFilt for Nanopore reads.| integer | 100 | | | trim_maxlen | Maximum length of reads

Help

Only applies to Nanopore reads.

Corresponds to the –maxlength option of NanoFilt.

| integer | 0 | | | trim_adapters | Sequences to be removed during trimming

Help

Only applies to Illumina reads. Corresponds to the first ILLUMINACLIP option of Trimmomatic. If left blank (i.e. --trim_adapters ''), then adapter trimming is disabled. Custom adapters cannot be used, and the parameter corresponds to one of the prebuilt sequence files provided with Trimmomatic.

| string | NexteraPE-PE.fa | | | trim_mismatches | Max number of base mismatches to allow an adapter match

Help

Only applies to Illumina reads. Corresponds to the second ILLUMINACLIP option of Trimmomatic.

| integer | 2 | | | trim_pclip | How accurate the match between adapter ligated reads must be for paired-end palindrome read alignment

Help

Only applies to Illumina reads. Corresponds to the third ILLUMINACLIP option of Trimmomatic.

| integer | 30 | | | trim_clip | How accurate the match between any adapter must be against a read

Help

Only applies to Illumina reads. Corresponds to the final ILLUMINACLIP option of Trimmomatic.

| integer | 10 | | | trim_winsize | Number of bases to average quality across

Help

Only applies to Illumina reads. If set to 0, then sliding window trimming is disabled. Corresponds to the first SLIDINGWINDOW option of Trimmomatic.

| integer | 50 | | | trim_winqual | Required average window base quality

Help

Only applies to Illumina reads. If set to 0, then sliding window trimming is disabled. Corresponds to the second SLIDINGWINDOW option of Trimmomatic.

| integer | 15 | | | trim_leading | Minimum quality of bases in leading end of read

Help

Only applies to Illumina reads. If set to 0, LEADING trimming is disabled. Corresponds to the LEADING option of Trimmomatic.

| integer | 15 | | | trim_trailing | Minimum quality of bases in trailing end of read

Help

Only applies to Illumina reads. If set to 0, TRAILING trimming is disabled. Corresponds to the TRAILING option of Trimmomatic.

| integer | 15 | | | trim_headcrop | Number of bases to remove from start of read

Help

Corresponds to the HEADCROP option of Trimmomatic for Illumina reads. If set to 0, then HEADCROP trimming is disabled.

Corresponds to the –headcrop option of NanoFilt for Nanopore reads.

| integer | 0 | | | trim_crop | Number of bases to keep from start of read

Help

Only applies to Illumina reads. If set to 0, CROP trimming is disabled. Corresponds to the CROP option of Trimmomatic.

| integer | 0 | | | trim_meanqual | Minimum average base quality of entire reads

Help

Applies only to ONT reads. Corresponds to the –quality option of NanoFilt.

| integer | 7 | | | trim_mingc | Minimum GC count of reads

Help

Only applies to ONT reads. Corresponds to the –minGC option of NanoFilt.

| integer | 0 | | | trim_maxgc | Maximum GC count of reads

Help

Only applies to ONT reads. Corresponds to the –maxGC option of NanoFilt.

| integer | 0 | | | trim_tailcrop | Number of bases to remove from the end of each read

Help

Only applies to ONT reads. Corresponds to the –tailcrop option of NanoFilt.

| integer | 0 | |

Workflow options

Options to skip portions of the workflow

Parameter	Description	Type	Default	Required
skip_trimming	Skip read trimming (Trimmomatic/Nanofilt)	boolean
skip_qc	Skip FastQC	boolean
skip_blast	Skip BLASTing any reads	boolean

Max job request options

Set the top limit for requested resources for any single job.

Parameter	Description	Type	Default	Required
max_cpus	Maximum number of CPUs that can be requested for any single job. Help Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1	integer	16
max_memory	Maximum amount of memory that can be requested for any single job. Help 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'	string	128.GB
max_time	Maximum amount of time that can be requested for any single job. Help 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'	string	240.h
enable_conda	Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.	boolean