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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help
N E X T F L O W ~ version 26.04.3
Downloading plugin nf-schema@2.5.1
Launching `./main.nf` [infallible_visvesvaraya] revision: a18b2be4cd
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/bacass 2.7.0dev
------------------------------------------------------
Typical pipeline command:
nextflow run nf-core/bacass -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 tab-separated sample sheet
--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.
QC and Trim
--fastp_args [string] This can be used to pass arguments to [Fastp](https://github.com/OpenGene/fastp)
--save_trimmed [boolean] save trimmed files
--save_trimmed_fail [boolean] save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
--skip_fastqc [boolean] Skip FastQC
--skip_nanoplot [boolean] Skip Nanoplot
--skip_toulligqc [boolean] Skip ToulligQC
--skip_fastp [boolean] Skip FastP
--discard_trimmed_pass [boolean] Specify true to not write any reads that pass trimming thresholds.This can be used to use fastp for
the output report only. [default: false]
--long_reads_filtering [string] Tool for ONT read filtering [default: porechop]
--filtlong_args [string] Arguments for running Filtlong
--filtlong_minlen [integer] Minimun length for Filtlong to work [default: 10]
--rasusa [boolean] Use Rasusa to downsample reads to a target coverage [default: false]
--rasusa_coverage [integer] Target coverage for Rasusa read downsampling [default: 100]
Contamination Screening
--kraken2db [string] Path to Kraken2 database.
--kmerfinderdb [string] Path to the KmerFinder bacteria database (e.g. `/path_to/kmerfinder/`,
`/path_to/kmerfinder/bacteria/` or `/path_to/kmerfinder/bacteria.tar.gz`). Only taxonomic group
`bacteria` is supported. If a directory is provided, the pipeline auto-detects whether it already
includes the `bacteria/` level. See installation guidelines:
[https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/).
Example: `--kmerfinderdb
'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz'` (FTP download
is ~30GB and can be slow; prefer pre-downloading and passing a local `.tar.gz`). Older version:
[https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz](https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz).
--reference_fasta [string] Reference FASTA file.
--reference_gff [string] Reference GFF file.
Assembly parameters
--assembler [string] The assembler(s) to use for assembly. [default:
autocycler,canu,dragonflye,flye,megahit,miniasm,unicycler,raven]
--assembly_type [string] Which type of assembly to perform. (accepted: short, long, hybrid)
--unicycler_args [string] Extra arguments for Unicycler
--canu_mode [string] Allowed technologies for long read assembly with CANU. (accepted: -pacbio, -nanopore,
-pacbio-hifi, null)
--canu_args [string] This can be used to supply [extra options](https://canu.readthedocs.io/en/latest/quick-start.html)
to the Canu assembler. Will be ignored when other assemblers are used.
--dragonflye_args [string] Extra arguments for [Dragonflye](https://github.com/rpetit3/dragonflye#usage)
--megahit_args [string] Extra arguments for [MEGAHIT](https://github.com/voutcn/megahit#usage)
--autocycler_assemblers [string] What assemblers to use for autocycler [default: canu,flye,miniasm,raven]
--autocycler_subsample_count [integer] Number of subsets to assemble. [default: 4]
--autocycler_subsample_mindepth [integer] Minimum depth for subsets to assemble. [default: 25]
--autocycler_cluster_args [string] Arguments to autocycler cluster.
--flye_mode [string] Allowed technologies for long read assembly with Flye. (accepted: --pacbio-raw, --pacbio-corr,
--pacbio-hifi, --nano-raw, --nano-corr, --nano-hq) [default: --nano-raw]
BUSCO options
--busco_lineage [string] BUSCO lineage to use, you can use other BUSCO lineages, these are available in:
https://busco.ezlab.org/list_of_lineages.html [default: bacteria_odb10]
--busco_mode [string] BUSCO mode to use (accepted: genome, proteins, transcriptome) [default: genome]
--busco_db_path [string, null] Path to BUSCO database
--busco_config_file [string, null] Path to BUSCO config file
--busco_clean_intermediates [boolean] Clean intermediate BUSCO files [default: false]
Assembly Polishing
--polish_method [string] Which assembly polishing method to use. (accepted: medaka, nanopolish, none) [default: medaka]
Annotation
--annotation_tool [string] The annotation method to annotate the final assembly. (accepted: prokka, bakta, dfast, liftoff)
[default: prokka]
--prokka_args [string] Extra arguments for prokka annotation tool.
--prokka_proteins [string] FASTA file with protein sequences to be used as reference by PROKKA.
--baktadb [string] Path to Bakta database
--baktadb_download [boolean] Download Bakta database
--baktadb_download_args [string] This can be used to supply [extra options](https://github.com/oschwengers/bakta#database-download)
to the Bakta download module (accepted: --type light, --type full) [default: --type light]
--dfast_config [string] Specifies a configuration file for the [DFAST](https://github.com/nigyta/dfast_core) annotation
method. [default: assets/test_config_dfast.py]
--liftoff_ref_from_kmerfinder [boolean] Use the reference files (.fasta, .gff) from kmerfinder step for LIFTOFF.
Skipping Options
--skip_kraken2 [boolean] Skip running Kraken2 classifier on reads.
--skip_kmerfinder [boolean] Skip contamination analysis with
[Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/)
--skip_annotation [boolean] Skip annotating the assembly with Prokka /DFAST.
--skip_pycoqc [boolean] Skip running `PycoQC` on long read input.
--skip_busco [boolean] Skip BUSCO
--skip_polish [boolean] Skip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies.
--skip_multiqc [boolean] Skip MultiQC
Generic options
--multiqc_title [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.
--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 18 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------
* The pipeline
https://doi.org/10.5281/zenodo.2669428
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/bacass/blob/master/CITATIONS.md