nf-core/metatdenovo
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
1.0.1). The latest
stable release is
1.2.0
.
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$activate when using single end reads input
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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..
stringUse 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
booleanSpecify which assembler you would like to run, possible alternatives: megahit, rnaspades. default: megahit
stringPath to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.
stringFilter out contigs shorter than this.
integerSave the bam files from mapping
booleanSave the output from samtools
booleanPath to a protein fasta file
stringPath to a gff file
stringSpecify which ORF caller you would like to run, possible alternatives: prodigal, prokka, transdecoder, default: prodigal.
stringSpecify 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$Skip EGGNOG functional annotation
booleanSpecify EGGNOG database path
stringeggnogskip kofamscan run
booleanPath to a directory with KOfam files. Will be created if it doesn’t exist.
string./kofam/Directory with hmm files which will be searched for among ORFs
string^\S+Comma-separated list of hmm files which will be searched for among ORFs
string\S+hmm(\.gz)?specify which pattern hmm files end with
string*.hmmskip eukulele run
booleanSpecify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets
stringEUKulele database.
stringEUKulele database folder.
string./eukulele/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleanShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
boolean