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metatdenovo_help.txt
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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help
N E X T F L O W ~ version 26.03.1-edge
Launching `./main.nf` [mighty_volhard] revision: ebe5825fde
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/metatdenovo 1.3.1
------------------------------------------------------
Typical pipeline command:
nextflow run nf-core/metatdenovo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>
help message of that parameter will be printed.
or `--helpFull`.
Input/output options
--input [string] Path to comma-separated file containing information about the samples in the experiment.
--outdir [string] The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure.
--email [string] Email address for completion summary.
--multiqc_title [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.
Quality control options
--skip_qc [boolean] Skip all QC steps except for MultiQC.
--skip_fastqc [boolean] Skip FastQC.
trimming options
--clip_r1 [string] Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).
--clip_r2 [string] Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).
--three_prime_clip_r1 [string] Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been
performed.
--three_prime_clip_r2 [string] Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been
performed.
--save_trimmed [boolean] Save the trimmed FastQ files in the results directory.
--trim_nextseq [string] Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing
poly-G tails.
--skip_trimming [boolean] Skip the adapter trimming step.
Filtering options
--sequence_filter [string] Fasta file with sequences to filter away before running assembly etc..
--save_bbduk_fastq [boolean] Save the resulting fastq files from filtering [default: false]
Digital normalization options
--bbnorm [boolean] Perform normalization to reduce sequencing depth.
--bbnorm_target [integer] Reduce the number of reads for assembly average coverage of this number. [default: 100]
--bbnorm_min [integer] Reads with an apparent depth of under nx will be presumed to be errors and discarded [default:
5]
--save_bbnorm_fastq [boolean] Save the resulting fastq files from normalization [default: false]
Assembler options
--assembler [string] Specify the assembler to run. Possible alternatives: megahit, spades. (accepted: megahit,
spades)
--user_assembly [string] Path to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.
--user_assembly_name [string] Name to give to the user-provided assembly. [default: user_assembly]
--min_contig_length [integer] Filter out contigs shorter than this. [default: 0]
--spades_flavor [string] Select which type of assembly you want to make. Default: rna (accepted: rna, isolate, sc, meta,
plasmid, metaplasmid, metaviral, rnaviral) [default: rna]
--save_formatspades [boolean] Save the formatted spades fasta file
Mapping options
--save_bam [boolean] Save the bam files from mapping
--save_samtools [boolean] Save the output from samtools [default: true]
--bbmap_minid [number] Minimum identity needed to assign read to a contig [default: 0.9]
Orf Caller options
--orf_caller [string] Specify which ORF caller to run. Possible alternatives: prodigal, prokka, transdecoder. This needs
to be set unless the `--user_orfs_*` params are set. (accepted: prodigal, prokka, transdecoder)
--user_orfs_faa [string] Path to a protein fasta file for user-provided ORFs.
--user_orfs_gff [string] Path to a gff file for user-provided ORFs.
--user_orfs_name [string] Name to give to user-provided ORFs. [default: user_orfs]
--prodigal_trainingfile [string] Specify a training file for prodigal. By default prodigal will learn from the input sequences
Functional annotation options
--skip_eggnog [boolean] Skip EGGNOG functional annotation
--eggnog_dbpath [string] Specify EGGNOG database path [default: eggnog]
--skip_kofamscan [boolean] If enabled, skips the run of KofamScan.
--kofam_dir [string] Path to a directory with KOfam files. Will be created if it doesn't exist. [default: ./kofam/]
--hmmdir [string] Directory with hmm files which will be searched for among ORFs
--hmmfiles [string] Comma-separated list of hmm files which will be searched for among ORFs
--hmmpattern [string] Specify which pattern hmm files end with [default: *.hmm]
Taxonomy annotation options
--diamond_dbs [string] Path to comma-separated file containing information about Diamond database files you want to use for
taxonomy assignment.
--diamond_top [integer] Argument to Diamond's `--top` that controls the percentage of hits to include in the LCA.
[default: 10]
--skip_eukulele [boolean] If enabled, skips the run of EUKulele
--eukulele_method [string] Specify which method to use for EUKulele. the alternatives are: mets (metatranscriptomics) or mags
(Metagenome Assembled Genomes). default: mets (accepted: mets, mags) [default: mets]
--eukulele_db [string] EUKulele database. (accepted: gtdb, phylodb, marmmetsp, mmetsp, eukprot)
--eukulele_dbpath [string] EUKulele database folder. [default: ./eukulele/]
Generic options
--multiqc_methods_description [string] Custom MultiQC yaml file containing HTML including a methods description.
--help [boolean, string] Display the help message.
--help_full [boolean] Display the full detailed help message.
--show_hidden [boolean] Display hidden parameters in the help message (only works when --help or --help_full are provided).
!! Hiding 19 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/metatdenovo/blob/master/CITATIONS.md