nf-core/mag
Assembly and binning of metagenomes
1.1.0
). The latest
stable release is
3.2.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files. Either this or the --manifest
parameter is required.
string
Use this to specify the location of your input FastQ files. For example:
--input 'path/to/data/sample_*_{1,2}.fastq'
Please note the following requirements:
- The path must be enclosed in quotes
- The path must have at least one
*
wildcard character - 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
Manifest file, required for hybrid assembly with metaSPAdes. Alternative to --input
.
string
Has 4 headerless columns (tab separated): Sample_Id, Long_Reads, Short_Reads_1, Short_Reads_2
Specifies that the input is single-end reads.
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.
string
./results
Email address for completion summary.
string
^([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.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
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.
boolean
Method used to save pipeline results to output directory.
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.
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.
string
^([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.
boolean
Set to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
If file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
boolean
Set to disable colourful command line output and live life in monochrome.
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${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.
integer
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.
string
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.
string
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.
string
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.
string
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.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
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.
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.
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.
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.
integer
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.
string
AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
Sequence of 3' adapter to remove in the reverse reads.
string
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Mean qualified quality value for keeping read.
integer
15
Trimming quality value for the sliding window.
integer
15
Name of iGenomes reference for host contamination removal.
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.
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--sensitive
setting for Bowtie 2 to map reads against the host genome.
boolean
Save the read IDs of removed host reads.
boolean
Keep reads similar to the Illumina internal standard PhiX genome.
boolean
Genome reference used to remove Illumina PhiX contaminant reads.
string
${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz
Skip removing adapter sequences from long reads.
boolean
Discard any read which is shorter than this value.
integer
1000
Keep this percent of bases.
integer
90
The higher the more important is read length when choosing the best reads.
integer
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.
boolean
Genome reference used to remove ONT Lambda contaminant reads.
string
${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.
string
E.g. "ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz".
Database for taxonomic binning with kraken2.
string
E.g. "ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz".
Skip creating a krona plot for taxonomic binning.
boolean
Database for taxonomic classification of metagenome assembled genomes.
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.
Skip Illumina-only SPAdes assembly.
boolean
Skip SPAdes hybrid assembly (only available when using manifest input).
boolean
Skip MEGAHIT assembly.
boolean
Skip metaQUAST.
boolean
Skip metagenome binning.
boolean
Minimum contig size to be considered for binning and for bin quality check.
integer
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.
integer
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.
integer
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.
boolean
Download path for BUSCO database.
string
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.
boolean
Useful to allow reproducibility, as BUSCO datasets are frequently updated and old versions do not always remain accessible.