nf-core/mag
Assembly and binning of metagenomes
3.2.0
). The latest
stable release is
4.0.0
.
Define where the pipeline should find input data and save output data.
CSV samplesheet file containing information about the samples in the experiment.
string
^\S+\.csv$
Specifies that the input is single-end reads.
boolean
Additional input CSV samplesheet containing information about pre-computed assemblies. When set, both read pre-processing and assembly are skipped and the pipeline begins at the binning stage.
string
^\S+\.csv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Reference genome related files and options required for the workflow.
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Use monochrome_logs
boolean
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
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
Fix number of CPUs used by SPAdes. Not increased with retries.
integer
-1
Fix number of CPUs used by SPAdes hybrid. Not increased with retries.
integer
-1
RNG seed for MetaBAT2.
integer
1
Specify which adapter clipping tool to use.
string
Specify to save the resulting clipped FASTQ files to —outdir.
boolean
The minimum length of reads must have to be retained for downstream analysis.
integer
15
Minimum phred quality value of a base to be qualified in fastp.
integer
15
The mean quality requirement used for per read sliding window cutting by fastp.
integer
15
Save reads that fail fastp filtering in a separate file. Not used downstream.
boolean
The minimum base quality for low-quality base trimming by AdapterRemoval.
integer
2
Turn on quality trimming by consecutive stretch of low quality bases, rather than by window.
boolean
Forward read adapter to be trimmed by AdapterRemoval.
string
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG
Reverse read adapter to be trimmed by AdapterRemoval for paired end data.
string
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
Name of iGenomes reference for host contamination removal.
string
Fasta reference file for host contamination removal.
string
Bowtie2 index directory corresponding to --host_fasta
reference file for host contamination removal.
string
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
Specify to save input FASTQ files with host reads removed to —outdir.
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 read preprocessing using fastp or adapterremoval.
boolean
Specify to save input FASTQ files with phiX reads removed to —outdir.
boolean
Run BBnorm to normalize sequence depth.
boolean
Set BBnorm target maximum depth to this number.
integer
100
Set BBnorm minimum depth to this number.
integer
5
Save normalized read files to output directory.
boolean
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
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
Specify to save input FASTQ files with lamba reads removed to —outdir.
boolean
Specify to save the resulting clipped FASTQ files to —outdir.
boolean
Specify to save the resulting length filtered FASTQ files to —outdir.
boolean
Specify which long read adapter trimming tool to use.
string
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
Database for taxonomic binning with kraken2.
string
Database for taxonomic binning with krona
string
Skip creating a krona plot for taxonomic binning.
boolean
Database for taxonomic classification of metagenome assembled genomes. Can be either a zipped file or a directory containing the extracted output of such.
string
Generate CAT database.
boolean
Save the CAT database generated when specified by --cat_db_generate
.
boolean
Only return official taxonomic ranks (Kingdom, Phylum, etc.) when running CAT.
boolean
Skip the running of GTDB, as well as the automatic download of the database
boolean
Specify the location of a GTDBTK database. Can be either an uncompressed directory or a .tar.gz
archive. If not specified will be downloaded for you when GTDBTK or binning QC is not skipped.
string
https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz
Specify the location of a GTDBTK mash database. If missing, GTDB-Tk will skip the ani_screening step
string
Min. bin completeness (in %) required to apply GTDB-tk classification.
number
50
Max. bin contamination (in %) allowed to apply GTDB-tk classification.
number
10
Min. fraction of AA (in %) in the MSA for bins to be kept.
number
10
Min. alignment fraction to consider closest genome.
number
0.65
Number of CPUs used for the by GTDB-Tk run tool pplacer.
integer
1
Speed up pplacer step of GTDB-Tk by loading to memory.
boolean
Database for virus classification with geNomad
string
Co-assemble samples within one group, instead of assembling each sample separately.
boolean
Additional custom options for SPAdes and SPAdesHybrid. Do not specify --meta
as this will be added for you!
string
Additional custom options for MEGAHIT.
string
Skip Illumina-only SPAdes assembly.
boolean
Skip SPAdes hybrid assembly.
boolean
Skip MEGAHIT assembly.
boolean
Skip metaQUAST.
boolean
Skip Prodigal gene prediction
boolean
Skip Prokka genome annotation.
boolean
Skip MetaEuk gene prediction and annotation
boolean
A string containing the name of one of the databases listed in the mmseqs2 documentation. This database will be downloaded and formatted for eukaryotic genome annotation. Incompatible with —metaeuk_db.
string
Path to either a local fasta file of protein sequences, or to a directory containing an mmseqs2-formatted database, for annotation of eukaryotic genomes.
string
Save the downloaded mmseqs2 database specified in --metaeuk_mmseqs_db
.
boolean
Run virus identification.
boolean
Minimum geNomad score for a sequence to be considered viral
number
0.7
Number of groups that geNomad’s MMSeqs2 databse should be split into (reduced memory requirements)
integer
1
Defines mapping strategy to compute co-abundances for binning, i.e. which samples will be mapped against the assembly.
string
Skip metagenome binning entirely
boolean
Skip MetaBAT2 Binning
boolean
Skip MaxBin2 Binning
boolean
Skip CONCOCT Binning
boolean
Minimum contig size to be considered for binning and for bin quality check.
integer
1500
Minimal length of contigs that are not part of any bin but treated as individual genome.
integer
1000000
Maximal number of contigs that are not part of any bin but treated as individual genome.
integer
100
Bowtie2 alignment mode
string
Save the output of mapping raw reads back to assembled contigs
boolean
Enable domain-level (prokaryote or eukaryote) classification of bins using Tiara. Processes which are domain-specific will then only receive bins matching the domain requirement.
boolean
Specify which tool to use for domain classification of bins. Currently only ‘tiara’ is implemented.
string
tiara
Minimum contig length for Tiara to use for domain classification. For accurate classification, should be longer than 3000 bp.
integer
3000
Disable bin QC with BUSCO or CheckM.
boolean
Specify which tool for bin quality-control validation to use.
string
Download URL for BUSCO lineage dataset, or path to a tar.gz archive, or local directory containing already downloaded and unpacked lineage datasets.
string
Run BUSCO with automated lineage selection, but ignoring eukaryotes (saves runtime).
boolean
Save the used BUSCO lineage datasets provided via --busco_db
.
boolean
Enable clean-up of temporary files created during BUSCO runs.
boolean
URL pointing to checkM database for auto download, if local path not supplied.
string
https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz
Path to local folder containing already downloaded and uncompressed CheckM database.
string
Save the used CheckM reference files downloaded when not using —checkm_db parameter.
boolean
Turn on bin refinement using DAS Tool.
boolean
Specify single-copy gene score threshold for bin refinement.
number
0.5
Specify which binning output is sent for downstream annotation, taxonomic classification, bin quality control etc.
string
Turn on GUNC genome chimerism checks
boolean
Specify a path to a pre-downloaded GUNC dmnd database file
string
Specify which database to auto-download if not supplying own
string
Save the used GUNC reference files downloaded when not using —gunc_db parameter.
boolean
Performs ancient DNA assembly validation and contig consensus sequence recalling.
Turn on/off the ancient DNA subworfklow
boolean
PyDamage accuracy threshold
number
0.5
deactivate damage correction of ancient contigs using variant and consensus calling
boolean
Ploidy for variant calling
integer
1
minimum base quality required for variant calling
integer
20
minimum minor allele frequency for considering variants
number
0.33
minimum genotype quality for considering a variant high quality
integer
30
minimum genotype quality for considering a variant medium quality
integer
20
minimum number of bases supporting the alternative allele
integer
3