nf-core/mag

Input FastQ files or CSV samplesheet file containing information about the samples in the experiment.

Specifies that the input is single-end reads.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Custom MultiQC yaml file containing HTML including a methods description.

Fix number of CPUs for MEGAHIT to 1. Not increased with retries.

Fix number of CPUs used by SPAdes. Not increased with retries.

Fix number of CPUs used by SPAdes hybrid. Not increased with retries.

RNG seed for MetaBAT2.

Specify which adapter clipping tool to use.

Specify to save the resulting clipped FASTQ files to —outdir.

The minimum length of reads must have to be retained for downstream analysis.

Minimum phred quality value of a base to be qualified in fastp.

The mean quality requirement used for per read sliding window cutting by fastp.

Save reads that fail fastp filtering in a separate file. Not used downstream.

The minimum base quality for low-quality base trimming by AdapterRemoval.

Turn on quality trimming by consecutive stretch of low quality bases, rather than by window.

Forward read adapter to be trimmed by AdapterRemoval.

Reverse read adapter to be trimmed by AdapterRemoval for paired end data.

Name of iGenomes reference for host contamination removal.

Fasta reference file for host contamination removal.

Use the --very-sensitive instead of the--sensitivesetting for Bowtie 2 to map reads against the host genome.

Save the read IDs of removed host reads.

Specify to save input FASTQ files with host reads removed to —outdir.

Keep reads similar to the Illumina internal standard PhiX genome.

Skip read preprocessing using fastp or adapterremoval.

Specify to save input FASTQ files with phiX reads removed to —outdir.

Skip removing adapter sequences from long reads.

Discard any read which is shorter than this value.

Keep this percent of bases.

The higher the more important is read length when choosing the best reads.

Keep reads similar to the ONT internal standard Escherichia virus Lambda genome.

Specify to save input FASTQ files with lamba reads removed to —outdir.

Specify to save the resulting clipped FASTQ files to —outdir.

Specify to save the resulting length filtered FASTQ files to —outdir.

Database for taxonomic binning with centrifuge.

Database for taxonomic binning with kraken2.

Skip creating a krona plot for taxonomic binning.

Database for taxonomic classification of metagenome assembled genomes. Can be either a zipped file or a directory containing the extracted output of such.

Generate CAT database.

Save the CAT database generated when specified by --cat_db_generate.

Only return official taxonomic ranks (Kingdom, Phylum, etc.) when running CAT.

GTDB database for taxonomic classification of bins with GTDB-tk.

Min. bin completeness (in %) required to apply GTDB-tk classification.

Max. bin contamination (in %) allowed to apply GTDB-tk classification.

Min. fraction of AA (in %) in the MSA for bins to be kept.

Min. alignment fraction to consider closest genome.

Number of CPUs used for the by GTDB-Tk run tool pplacer.

Reduce GTDB-Tk memory consumption by running pplacer in a setting writing to disk.

Co-assemble samples within one group, instead of assembling each sample separately.

Additional custom options for SPAdes.

Additional custom options for MEGAHIT.

Skip Illumina-only SPAdes assembly.

Skip SPAdes hybrid assembly.

Skip MEGAHIT assembly.

Skip metaQUAST.

Skip Prodigal gene prediction

Defines mapping strategy to compute co-abundances for binning, i.e. which samples will be mapped against the assembly.

Skip metagenome binning entirely

Skip MetaBAT2 Binning

Skip MaxBin2 Binning

Skip CONCOCT Binning

Minimum contig size to be considered for binning and for bin quality check.

Minimal length of contigs that are not part of any bin but treated as individual genome.

Maximal number of contigs that are not part of any bin but treated as individual genome.

Bowtie2 alignment mode

Skip Prokka genome annotation.

Disable bin QC with BUSCO or CheckM.

Specify which tool for bin quality-control validation to use.

Download path for BUSCO lineage dataset, instead of using automated lineage selection.

Path to local folder containing already downloaded and unpacked lineage datasets.

Run BUSCO with automated lineage selection, but ignoring eukaryotes (saves runtime).

Save the used BUSCO lineage datasets provided via —busco_reference or downloaded when not using —busco_reference or —busco_download_path.

Enable clean-up of temporary files created during BUSCO runs.

Path to local folder containing already downloaded and uncompressed CheckM database.

Save the used CheckM reference files downloaded when not using —checkm_db parameter.

Turn on bin refinement using DAS Tool.

Specify single-copy gene score threshold for bin refinement.

Specify which binning output is sent for downstream annotation, taxonomic classification, bin quality control etc.

Turn on GUNC genome chimerism checks

Specify a path to a pre-downloaded GUNC dmnd database file

Specify which database to auto-download if not supplying own

Save the used GUNC reference files downloaded when not using —gunc_db parameter.

Turn on/off the ancient DNA subworfklow

Ploidy for variant calling

minimum base quality required for variant calling

minimum minor allele frequency for considering variants

minimum genotype quality for considering a variant high quality

minimum genotype quality for considering a variant medium quality

minimum number of bases supporting the alternative allele

PyDamage accuracy threshold