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

Input FastQ files or TSV file.

type: string

Use this to specify the location of your input FastQ files. For example:

--input 'path/to/data/sample_*_{1,2}.fastq'  

All files will get assigned the same group ID (by default only used to compute co-abundances for binning). Please note the following requirements:

  1. The path must be enclosed in quotes
  2. The path must have at least one * wildcard character
  3. When using the pipeline with paired end data, the path must use {1,2} notation to specify read pairs.

If left unspecified, a default pattern is used: data/*{1,2}.fastq.gz.

Alternatively, to assign different groups or to include long reads for hybrid assembly with metaSPAdes, you can specify a TSV input file (requires a '.tsv' suffix) with 4 or 5 headerless columns: Sample_Id, Group_Id, Short_Reads_1, Short_Reads_2 [, Long_Reads].

Paths to input FastQ files for tests.

hidden
type: string

Specifies that the input is single-end reads.

type: boolean

By default, the pipeline expects paired-end data. If you have single-end data, you need to specify --single_end on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for --input. For example:

--single_end --input '*.fastq'  

It is not possible to run a mixture of single-end and paired-end files in one run.

The output directory where the results will be saved.

type: string
default: ./results

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

Options for the reference genome indices used to align reads.

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Do not load the iGenomes reference config.

hidden
type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

Workflow name.

hidden
type: string

A custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

This works exactly as with --email, except emails are only sent if the workflow is not successful.

Send plain-text email instead of HTML.

hidden
type: boolean

Set to receive plain-text e-mails instead of HTML formatted.

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

If file generated by pipeline exceeds the threshold, it will not be attached.

Do not use coloured log outputs.

hidden
type: boolean

Set to disable colourful command line output and live life in monochrome.

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

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

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB

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'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h

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'

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Provide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.

## Download and use config file with following git commit id  
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96  

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

If you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the custom_config_base option. For example:

## Download and unzip the config files  
cd /path/to/my/configs  
wget https://github.com/nf-core/configs/archive/master.zip  
unzip master.zip  
  
## Run the pipeline  
cd /path/to/my/data  
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/  

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.

Institutional configs hostname.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Use these parameters to also enable reproducible results from the individual assembly and binning tools .

Fix number of CPUs for MEGAHIT to 1. Not increased with retries.

type: boolean

MEGAHIT only generates reproducible results when run single-threaded.

When using this parameter do not change the number of CPUs for the megahit process with a custom config file. This would result in an error.

Default: The number of CPUs is specified in the base.config file, and increased with each retry.

Fix number of CPUs used by SPAdes. Not increased with retries.

type: integer

SPAdes is designed to be deterministic for a given number of threads. To generate reproducible results fix the number of CPUs using this parameter.

When using this parameter do not change the number of CPUs for the spades process with a custom config file. This would result in an error.

Default: The number of CPUs is specified in the base.config file, and increased with each retry.

Fix number of CPUs used by SPAdes hybrid. Not increased with retries.

type: integer

SPAdes is designed to be deterministic for a given number of threads. To generate reproducible results fix the number of CPUs using this parameter.

When using this parameter do not change the number of CPUs for the spadeshybrid process with a custom config file. This would result in an error.

Default: The number of CPUs is specified in the base.config file, and increased with each retry.

RNG seed for MetaBAT2.

type: integer
default: 1

MetaBAT2 is run by default with a fixed seed within this pipeline, thus producing reproducible results. You can set it also to any other positive integer to ensure reproducibility. Set the parameter to 0 to use a random seed.

Sequence of 3' adapter to remove in the forward reads.

type: string
default: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

Sequence of 3' adapter to remove in the reverse reads.

type: string
default: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

Mean qualified quality value for keeping read.

type: integer
default: 15

Trimming quality value for the sliding window.

type: integer
default: 15

Name of iGenomes reference for host contamination removal.

type: string

This parameter is mutually exclusive with --host_genome. Host read removal is done with Bowtie2.
Both the iGenomes FASTA file as well as corresponding, already pre-built Bowtie 2 index files will be used.

Fasta reference file for host contamination removal.

type: string

This parameter is mutually exclusive with --host_fasta. The reference can be masked. Host read removal is done with Bowtie2.

Use the --very-sensitive instead of the--sensitivesetting for Bowtie 2 to map reads against the host genome.

type: boolean

Save the read IDs of removed host reads.

type: boolean

Keep reads similar to the Illumina internal standard PhiX genome.

type: boolean

Genome reference used to remove Illumina PhiX contaminant reads.

hidden
type: string
default: ${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz

Skip removing adapter sequences from long reads.

type: boolean

Discard any read which is shorter than this value.

type: integer
default: 1000

Keep this percent of bases.

type: integer
default: 90

The higher the more important is read length when choosing the best reads.

type: integer
default: 10

The default value focuses on length instead of quality to improve assembly size.
In order to assign equal weights to read lengths and read qualities set this parameter to 1.
This might be useful, for example, to benefit indirectly from the removal of short host reads (causing lower qualities for reads not overlapping filtered short reads).

Keep reads similar to the ONT internal standard Escherichia virus Lambda genome.

type: boolean

Genome reference used to remove ONT Lambda contaminant reads.

hidden
type: string
default: ${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz

Taxonomic classification is disabled by default. You have to specify one of the options below to activate it.

Database for taxonomic binning with centrifuge.

type: string

E.g. "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz".

Database for taxonomic binning with kraken2.

type: string

E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz".

Skip creating a krona plot for taxonomic binning.

type: boolean

Database for taxonomic classification of metagenome assembled genomes.

type: string

E.g. "http://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20200304.tar.gz".
The zipped file needs to contain a folder named "taxonomy" and "CAT_database" that hold the respective files.

Co-assemble samples within one group, instead of assembling each sample separately.

type: boolean

Additional custom options for SPAdes.

type: string
default: ""

An example is adjusting k-mers ("-k 21,33,55,77") or adding advanced options. But not -t, -m, -o or --out-prefix, because these are already in use.

Additional custom options for MEGAHIT.

type: string
default: ""

An example is adjusting presets (e.g. "--presets meta-large"), k-mers (e.g. "-k 21,33,55,77") or adding other advanced options. For example, increase the minimum k-mer in the event of an error message such as "Too many vertices in the unitig graph, you may increase the kmer size to remove tons of erroneous kmers." in the MEGAHIT log file. But not --threads, --memory, -o or input read files, because these are already in use.

Skip Illumina-only SPAdes assembly.

type: boolean

Skip SPAdes hybrid assembly.

type: boolean

Skip MEGAHIT assembly.

type: boolean

Skip metaQUAST.

type: boolean

Defines mapping strategy to compute co-abundances for binning, i.e. which samples will be mapped against the assembly.

type: string
default: group

Available: all, group or own. Note that own cannot be specified in combination with --coassemble_group.

Note that specifying all without additionally specifying --coassemble_group results in n^2 mapping processes for each assembly method, where n is the number of samples.

Skip metagenome binning.

type: boolean

Minimum contig size to be considered for binning and for bin quality check.

type: integer
default: 1500

For forwarding into downstream analysis, i.e. QUAST and BUSCO, and reporting.

Minimal length of contigs that are not part of any bin but treated as individual genome.

type: integer
default: 1000000

Contigs that do not fulfill the thresholds of --min_length_unbinned_contigs and --max_unbinned_contigs are pooled for downstream analysis and reporting, except contigs that also do not fullfill --min_contig_size are not considered further.

Maximal number of contigs that are not part of any bin but treated as individual genome.

type: integer
default: 100

Contigs that do not fulfill the thresholds of --min_length_unbinned_contigs and --max_unbinned_contigs are pooled for downstream analysis and reporting, except contigs that also do not fullfill --min_contig_size are not considered further.

Disable bin QC with BUSCO.

type: boolean

Download path for BUSCO database.

type: string
default: https://busco-data.ezlab.org/v4/data/lineages/bacteria_odb10.2020-03-06.tar.gz

Available databases are listed here: https://busco.ezlab.org/.

Save BUSCO reference.

type: boolean

Useful to allow reproducibility, as BUSCO datasets are frequently updated and old versions do not always remain accessible.

hidden
type: string