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$
Activate when using single end reads input
boolean
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Option for QC steps
Skip all QC steps except for MultiQC.
boolean
Skip FastQC.
boolean
all the trim option are listed below
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
string
Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
string
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
string
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
string
Save the trimmed FastQ files in the results directory.
boolean
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
string
Skip the adapter trimming step.
boolean
Fasta file with sequences to filter away before running assembly etc..
string
Save the resulting fastq files from filtering
boolean
false
Use these option if you need to normalize the reads before the assembly
Perform normalization to reduce sequencing depth.
boolean
Reduce the number of reads for assembly average coverage of this number.
integer
100
Reads with an apparent depth of under nx will be presumed to be errors and discarded
integer
5
Save the resulting fastq files from normalization
boolean
false
Specify the assembler to run. Possible alternatives: megahit, spades.
string
Path to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.
string
Name to give to the user-provided assembly.
string
user_assembly
Filter out contigs shorter than this.
integer
Select which type of assembly you want to make. Default: rna
string
Save the formatted spades fasta file
boolean
Save the bam files from mapping
boolean
Save the output from samtools
boolean
true
Minimum identity needed to assign read to a contig
number
0.9
Specify which ORF caller to run. Possible alternatives: prodigal, prokka, transdecoder. This needs to be set unless the --user_orfs_*
params are set.
string
Path to a protein fasta file for user-provided ORFs.
string
Path to a gff file for user-provided ORFs.
string
Name to give to user-provided ORFs.
string
user_orfs
Specify a training file for prodigal. By default prodigal will learn from the input sequences
string
Size of individual files annotated by Prokka in one batch.
string
10 MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Skip EGGNOG functional annotation
boolean
Specify EGGNOG database path
string
eggnog
If enabled, skips the run of KofamScan.
boolean
Path 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
*.hmm
Path 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.
integer
10
If enabled, skips the run of EUKulele
boolean
Specify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags (Metagenome Assembled Genomes). default: mets
string
EUKulele database.
string
EUKulele database folder.
string
./eukulele/
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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