nf-core/metatdenovo
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOption for QC steps
Skip all QC steps except for MultiQC.
booleanSkip FastQC.
booleanall the trim option are listed below
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
stringInstructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
stringInstructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
stringInstructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
stringSave the trimmed FastQ files in the results directory.
booleanInstructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
stringSkip the adapter trimming step.
booleanFasta file with sequences to filter away before running assembly etc..
stringSave the resulting fastq files from filtering
booleanfalseUse these option if you need to normalize the reads before the assembly
Perform normalization to reduce sequencing depth.
booleanReduce the number of reads for assembly average coverage of this number.
integer100Reads with an apparent depth of under nx will be presumed to be errors and discarded
integer5Save the resulting fastq files from normalization
booleanfalseSpecify the assembler to run. Possible alternatives: megahit, spades.
stringPath to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.
stringName to give to the user-provided assembly.
stringuser_assemblyFilter out contigs shorter than this.
integerSelect which type of assembly you want to make. Default: rna
stringSave the formatted spades fasta file
booleanSave the bam files from mapping
booleanSave the output from samtools
booleantrueMinimum identity needed to assign read to a contig
number0.9Specify which ORF caller to run. Possible alternatives: prodigal, prokka, transdecoder. This needs to be set unless the --user_orfs_* params are set.
stringPath to a protein fasta file for user-provided ORFs.
stringPath to a gff file for user-provided ORFs.
stringName to give to user-provided ORFs.
stringuser_orfsSpecify a training file for prodigal. By default prodigal will learn from the input sequences
stringSize of individual files annotated by Prokka in one batch.
string10 MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Skip EGGNOG functional annotation
booleanSpecify EGGNOG database path
stringeggnogIf enabled, skips the run of KofamScan.
booleanPath to a directory with KOfam files. Will be created if it doesn’t exist.
string./kofam/Directory with hmm files which will be searched for among ORFs
string^\S+Comma-separated list of hmm files which will be searched for among ORFs
string\S+hmm(\.gz)?Specify which pattern hmm files end with
string*.hmmPath to comma-separated file containing information about Diamond database files you want to use for taxonomy assignment.
string^\S+\.(csv|tsv|json|yaml|yml)$Argument to Diamond’s --top that controls the percentage of hits to include in the LCA.
integer10If enabled, skips the run of EUKulele
booleanSpecify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets
stringEUKulele database.
stringEUKulele database folder.
string./eukulele/Parameters 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.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
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.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string