nf-core/mag
Assembly and binning of metagenomes
1.1.0). The latest
stable release is
4.0.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files. Either this or the --manifest parameter is required.
stringManifest file, required for hybrid assembly with metaSPAdes. Alternative to --input.
stringSpecifies that the input is single-end reads.
booleanThe 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})$Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GBMaximum amount of time that can be requested for any single job.
string240.hParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringUse these parameters to also enable reproducible results from the individual assembly and binning tools .
Fix number of CPUs for MEGAHIT to 1. Not increased with retries.
booleanFix number of CPUs used by SPAdes. Not increased with retries.
integerFix number of CPUs used by SPAdes hybrid. Not increased with retries.
integerRNG seed for MetaBAT2.
integer1Sequence of 3’ adapter to remove in the forward reads.
stringAGATCGGAAGAGCACACGTCTGAACTCCAGTCASequence of 3’ adapter to remove in the reverse reads.
stringAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTMean qualified quality value for keeping read.
integer15Trimming quality value for the sliding window.
integer15Name of iGenomes reference for host contamination removal.
stringFasta reference file for host contamination removal.
stringUse the --very-sensitive instead of the--sensitivesetting for Bowtie 2 to map reads against the host genome.
booleanSave the read IDs of removed host reads.
booleanKeep reads similar to the Illumina internal standard PhiX genome.
booleanGenome reference used to remove Illumina PhiX contaminant reads.
string${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.
stringSkip Illumina-only SPAdes assembly.
booleanSkip SPAdes hybrid assembly (only available when using manifest input).
booleanSkip MEGAHIT assembly.
booleanSkip metaQUAST.
booleanSkip metagenome 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.
integer100Disable bin QC with BUSCO.
booleanDownload path for BUSCO database.
stringhttps://busco-data.ezlab.org/v4/data/lineages/bacteria_odb10.2020-03-06.tar.gzSave BUSCO reference.
boolean