nf-core/mag
Assembly and binning of metagenomes
2.0.0). The latest
stable release is
3.2.1
.
Define where the pipeline should find input data and save output data.
Input FastQ files or CSV samplesheet file.
stringUse this to specify the location of your input FastQ files. For example:
--input 'path/to/data/sample_*_{1,2}.fastq.gz'
Alternatively, to assign different groups or to include long reads for hybrid assembly with metaSPAdes, you can specify a CSV samplesheet input file with 5 columns and the following header: sample,group,short_reads_1,short_reads_2,long_reads. See usage docs.
Specifies that the input is single-end reads.
booleanBy 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./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Boolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
booleanCustom config file to supply to MultiQC.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoRun this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.
booleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
booleanThis may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues.
Show all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$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.
stringmasterProvide 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.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringUse 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.
booleanMEGAHIT 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-1SPAdes 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: -1 (the number of CPUs is specified in the base.config or in a custom config file, and increased with each retry).
Fix number of CPUs used by SPAdes hybrid. Not increased with retries.
integer-1SPAdes 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: -1 (the number of CPUs is specified in the base.config or in a custom config file, and increased with each retry).
RNG seed for MetaBAT2.
integer1MetaBAT2 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.
Save the by fastp trimmed FastQ files in the results directory.
booleanBy default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
Minimum phred quality value of a base to be qualified.
integer15The mean quality requirement used for per read sliding window cutting by fastp.
integer15Name of iGenomes reference for host contamination removal.
stringThis 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.
stringThis 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.
booleanSave the read IDs of removed host reads.
booleanKeep reads similar to the Illumina internal standard PhiX genome.
booleanGenome reference used to remove Illumina PhiX contaminant reads.
string${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gzSkip removing adapter sequences from long reads.
booleanDiscard any read which is shorter than this value.
integer1000Keep this percent of bases.
integer90The higher the more important is read length when choosing the best reads.
integer10The 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.
booleanGenome reference used to remove ONT Lambda contaminant reads.
string${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gzTaxonomic classification is disabled by default. You have to specify one of the options below to activate it.
Database for taxonomic binning with centrifuge.
stringE.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz.
Database for taxonomic binning with kraken2.
stringThe database file must be a compressed tar archive that contains at least the three files hash.k2d, opts.k2d and taxo.k2d. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz.
Skip creating a krona plot for taxonomic binning.
booleanDatabase for taxonomic classification of metagenome assembled genomes.
stringE.g. https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz. This parameter is mutually exclusive with --cat_db_generate. The zipped file needs to contain a folder named *taxonomy* and *database* that hold the respective files.
Generate CAT database.
booleanDownload the taxonomy files from NCBI taxonomy, the nr database and generate CAT database. This parameter is mutually exclusive with --cat_db. Useful to build a CAT database with the same DIAMOND version as used for running CAT classification, avoiding compatibility problems.
Save the CAT database generated when specified by --cat_db_generate.
booleanUseful to allow reproducibility, as old versions of prebuild CAT databases do not always remain accessible and underlying NCBI taxonomy and nr databases change.
GTDB database for taxonomic classification of bins with GTDB-tk.
stringhttps://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gzFor information which GTDB reference databases are compatible with the used GTDB-tk version see https://ecogenomics.github.io/GTDBTk/installing/index.html#gtdb-tk-reference-data.
Min. bin completeness (in %) required to apply GTDB-tk classification.
number50Completeness assessed with BUSCO analysis (100% - %Missing). Must be greater than 0 (min. 0.01) to avoid GTDB-tk errors. If too low, GTDB-tk classification results can be impaired due to not enough marker genes!
Max. bin contamination (in %) allowed to apply GTDB-tk classification.
number10Contamination approximated based on BUSCO analysis (%Complete and duplicated). If too high, GTDB-tk classification results can be impaired due to contamination!
Min. fraction of AA (in %) in the MSA for bins to be kept.
number10Min. alignment fraction to consider closest genome.
number0.65Number of CPUs used for the by GTDB-Tk run tool pplacer.
number1A low number of CPUs helps to reduce the memory required/reported by GTDB-Tk. See also the GTDB-Tk documentation.
Reduce GTDB-Tk memory consumption by running pplacer in a setting writing to disk.
booleantrueWill be slower. Set to false to turn this off.
Co-assemble samples within one group, instead of assembling each sample separately.
booleanAdditional custom options for SPAdes.
stringAn 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.
stringAn 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.
booleanSkip SPAdes hybrid assembly.
booleanSkip MEGAHIT assembly.
booleanSkip metaQUAST.
booleanDefines mapping strategy to compute co-abundances for binning, i.e. which samples will be mapped against the assembly.
stringgroupAvailable: 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.
booleanMinimum contig size to be considered for binning and for bin quality check.
integer1500For 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.
integer1000000Contigs 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.
integer100Contigs 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.
booleanDownload path for BUSCO lineage dataset, instead of using automated lineage selection.
stringE.g. https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz. Available databases are listed here: https://busco-data.ezlab.org/v5/data/lineages/.
Path to local folder containing already downloaded and unpacked lineage datasets.
stringIf provided, BUSCO analysis will be run in offline mode. Data can be downloaded from https://busco-data.ezlab.org/v5/data/ (files still need to be unpacked manually). Run in combination with automated lineage selection.
Run BUSCO with automated lineage selection, but ignoring eukaryotes (saves runtime).
booleanSave the used BUSCO lineage datasets provided via --busco_reference or downloaded when not using --busco_reference or --busco_download_path.
booleanUseful to allow reproducibility, as BUSCO datasets are frequently updated and old versions do not always remain accessible.