nf-core/mag
Assembly and binning of metagenomes
2.2.1). The latest
stable release is
4.0.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files or CSV samplesheet file containing information about the samples in the experiment.
stringSpecifies that the input is single-end reads.
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanUse 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.
booleanFix number of CPUs used by SPAdes. Not increased with retries.
integer-1Fix number of CPUs used by SPAdes hybrid. Not increased with retries.
integer-1RNG seed for MetaBAT2.
integer1Specify which adapter clipping tool to use. Options: ‘fastp’, ‘adapterremoval’
stringThe minimum length of reads must have to be retained for downstream analysis.
integer15Minimum phred quality value of a base to be qualified in fastp.
integer15The mean quality requirement used for per read sliding window cutting by fastp.
integer15Save reads that fail fastp filtering in a separate file. Not used downstream.
booleanThe minimum base quality for low-quality base trimming by AdapterRemoval.
integer2Turn on quality trimming by consecutive stretch of low quality bases, rather than by window.
booleanForward read adapter to be trimmed by AdapterRemoval.
stringAGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTGReverse read adapter to be trimmed by AdapterRemoval for paired end data.
stringAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTName of iGenomes reference for host contamination removal.
stringFasta reference file for host contamination removal.
stringUse 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${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gzSkip removing adapter sequences from long reads.
booleanDiscard any read which is shorter than this value.
integer1000Keep this percent of bases.
integer90The higher the more important is read length when choosing the best reads.
integer10Keep reads similar to the ONT internal standard Escherichia virus Lambda genome.
booleanGenome reference used to remove ONT Lambda contaminant reads.
string${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.
stringDatabase for taxonomic binning with kraken2.
stringSkip creating a krona plot for taxonomic binning.
booleanDatabase for taxonomic classification of metagenome assembled genomes.
stringGenerate CAT database.
booleanSave the CAT database generated when specified by --cat_db_generate.
booleanGTDB database for taxonomic classification of bins with GTDB-tk.
stringhttps://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gzMin. bin completeness (in %) required to apply GTDB-tk classification.
number50Max. bin contamination (in %) allowed to apply GTDB-tk classification.
number10Min. 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.
number1Reduce GTDB-Tk memory consumption by running pplacer in a setting writing to disk.
booleantrueCo-assemble samples within one group, instead of assembling each sample separately.
booleanAdditional custom options for SPAdes.
stringAdditional custom options for MEGAHIT.
stringSkip Illumina-only SPAdes assembly.
booleanSkip SPAdes hybrid assembly.
booleanSkip MEGAHIT assembly.
booleanSkip metaQUAST.
booleanSkip Prodigal gene prediction
booleanDefines mapping strategy to compute co-abundances for binning, i.e. which samples will be mapped against the assembly.
stringgroupSkip metagenome binning entirely
booleanSkip MetaBAT2 Binning
booleanSkip MaxBin2 Binning
booleanMinimum contig size to be considered for binning and for bin quality check.
integer1500Minimal length of contigs that are not part of any bin but treated as individual genome.
integer1000000Maximal number of contigs that are not part of any bin but treated as individual genome.
integer100Bowtie2 alignment mode
stringSkip Prokka genome annotation.
booleanDisable bin QC with BUSCO.
booleanDownload path for BUSCO lineage dataset, instead of using automated lineage selection.
stringPath to local folder containing already downloaded and unpacked lineage datasets.
stringRun 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.
booleanTurn on bin refinement using DAS Tool.
booleanSpecify single-copy gene score threshold for bin refinement.
number0.5Specify which binning output is sent for downstream annotation, taxonomic classification, bin quality control etc.
stringPerforms ancient DNA assembly validation and contig consensus sequence recalling.
Turn on/off the ancient DNA subworfklow
booleanPloidy for variant calling
integer1minimum base quality required for variant calling
integer20minimum minor allele frequency for considering variants
number0.33minimum genotype quality for considering a variant high quality
integer30minimum genotype quality for considering a variant medium quality
integer20minimum number of bases supporting the alternative allele
integer3PyDamage accuracy threshold
number0.5