nf-core/createtaxdb
Parallelised and automated construction of metagenomic classifier databases of different tools
Introduction
Samplesheet input
You will need to create a samplesheet with information about the reference sequences you would like to build into a database before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
--input '[path to samplesheet file]'Full samplesheet
A samplesheet for nf-core/createtaxdb should have a minimum of 3 columns.
The first two columns are mandatory for meta information about the reference sequences (a reference name and a taxon ID), and you must include one a minimum of one column specifying paths to a reference sequence in fasta format. You can also supply two path columns for both DNA and amino acid sequences, if you wish to build databases for both nucleotide and amino acid-based taxonomic profiling tools.
id,taxid,fasta_dna,fasta_aa
Severe_acute_respiratory_syndrome_coronavirus_2,2697049,/path/to/fna/sarscov2.fasta,/path/to/faa/sarscov2.faa
Haemophilus_influenzae,727,/path/to/fnahaemophilus_influenzae.fna.gz,| Column | Description |
|---|---|
id | Custom reference sequence name. |
taxid | A numeric taxonomy ID of the reference that corresponds to species the reference sequence is from, as specified in the supplied taxonomy |
fasta_dna | Full path to FastA file with nucleotide sequences. File may be uncompressed or gzipped and have the extension .fasta, .fna, .fas, .fa. |
fasta_aa | Full path to FastA file with amino acid sequences. File may be uncompressed or gzipped and have the extension .fasta, .faa, .fas, .fa. |
An example samplesheet has been provided with the pipeline.
Running the pipeline
The typical command for running the pipeline is as follows:
nextflow run nf-core/createtaxdb --input ./samplesheet.csv --outdir ./results -profile docker --dbname '<your database name>' --build_<supported tool name> --<supported tool name>_build_params '"-v"' <...>Where you activate the building of a particular database with --build_<supported tool name> and optionally customise the given tool’s build parameters wth --<supported tool_name>_build_parameters .
There is not a default tool the pipeline will build a database for. --build_<supported tool name> flag.
For all parameter options, see the parameters page.
Some tools may require or recommend additional files - such as taxonomy files - to execute. Please refer to this section for guidance.
This will launch the pipeline with the docker configuration profile. See below for more information about profiles.
Note that the pipeline will create the following files in your working directory:
work # Directory containing the nextflow working files
<OUTDIR> # Finished results in specified location (defined with --outdir)
.nextflow_log # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.Many of the building tools require uncompressed FASTA files and/or a single combined FASTA.
If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
Once the pipeline has run to completion, we highly recommend moving the resulting directories or tar files to a centralised ‘cache’ location.
If you do so, ensure to update the paths in any downstream samplesheets you create with the --generate_downstream_samplesheets parameter.
Pipeline settings can be provided in a yaml or json file via -params-file <file>.
Do not use -c <file> to specify parameters as this will result in errors. Custom config files specified with -c must only be used for tuning process resource specifications, other infrastructural tweaks (such as output directories), or module arguments (args).
The above pipeline run specified with a params file in yaml format:
nextflow run nf-core/createtaxdb -profile docker -params-file params.yamlwith:
input: './samplesheet.csv'
outdir: './results/'
<...>You can also generate such YAML/JSON files via nf-core/launch.
Updating the pipeline
When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you’re running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
nextflow pull nf-core/createtaxdbReproducibility
It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you’ll be running the same version of the pipeline, even if there have been changes to the code since.
First, go to the nf-core/createtaxdb releases page and find the latest pipeline version - numeric only (eg. 1.3.1). Then specify this when running the pipeline with -r (one hyphen) - eg. -r 1.3.1. Of course, you can switch to another version by changing the number after the -r flag.
This version number will be logged in reports when you run the pipeline, so that you’ll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
To further assist in reproducibility, you can use share and reuse parameter files to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
Core Nextflow arguments
These options are part of Nextflow and use a single hyphen (pipeline parameters use a double-hyphen)
-profile
Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
The pipeline also dynamically loads configurations from https://github.com/nf-core/configs when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the nf-core/configs documentation.
Note that multiple profiles can be loaded, for example: -profile test,docker - the order of arguments is important!
They are loaded in sequence, so later profiles can overwrite earlier profiles.
If -profile is not specified, the pipeline will run locally and expect all software to be installed and available on the PATH. This is not recommended, since it can lead to different results on different machines dependent on the computer environment.
test- A profile with a complete configuration for automated testing
- Includes links to test data so needs no other parameters
docker- A generic configuration profile to be used with Docker
singularity- A generic configuration profile to be used with Singularity
podman- A generic configuration profile to be used with Podman
shifter- A generic configuration profile to be used with Shifter
charliecloud- A generic configuration profile to be used with Charliecloud
apptainer- A generic configuration profile to be used with Apptainer
wave- A generic configuration profile to enable Wave containers. Use together with one of the above (requires Nextflow
24.03.0-edgeor later).
- A generic configuration profile to enable Wave containers. Use together with one of the above (requires Nextflow
conda- A generic configuration profile to be used with Conda. Please only use Conda as a last resort i.e. when it’s not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
-resume
Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files’ contents as well. For more info about this parameter, see this blog post.
You can also supply a run name to resume a specific run: -resume [run-name]. Use the nextflow log command to show previous run names.
-c
Specify the path to a specific config file (this is a core Nextflow command). See the nf-core website documentation for more information.
Custom configuration
Resource requests
Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified here it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
To change the resource requests, please see the max resources and tuning workflow resources section of the nf-core website.
Custom Containers
In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the biocontainers or bioconda projects. However, in some cases the pipeline specified version maybe out of date.
To use a different container from the default container or conda environment specified in a pipeline, please see the updating tool versions section of the nf-core website.
Custom Tool Arguments
A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
To learn how to provide additional arguments to a particular tool of the pipeline, please see the customising tool arguments section of the nf-core website.
nf-core/configs
In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the nf-core/configs git repository. Before you do this please can you test that the config file works with your pipeline of choice using the -c parameter. You can then create a pull request to the nf-core/configs repository with the addition of your config file, associated documentation file (see examples in nf-core/configs/docs), and amending nfcore_custom.config to include your custom profile.
See the main Nextflow documentation for more information about creating your own configuration files.
If you have any questions or issues please send us a message on Slack on the #configs channel.
Running in the background
Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
The Nextflow -bg flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file.
Alternatively, you can use screen / tmux or similar tool to create a detached session which you can log back into at a later time.
Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).
Nextflow memory requirements
In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
We recommend adding the following line to your environment to limit this (typically in ~/.bashrc or ~./bash_profile):
NXF_OPTS='-Xms1g -Xmx4g'Frequently Asked Questions
Recommended auxiliary files
Some tools may require or recommend additional files to the reference sequence files - such as taxonomy files - to execute.
We provide a list of required or recommended files, and which pipeline parameters to give them to here:
- bracken
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - (nucleotide) accession2taxid file (
--accession2taxid)
- taxonomy name dump file (
- centrifuge
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - nucl2taxid file (
--nucl2taxid)
- taxonomy name dump file (
- diamond
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - prot2taxid file (
--prot2taxid)
- taxonomy name dump file (
- ganon
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp)
- taxonomy name dump file (
- kaiju (no additional files required)
- kraken2
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - (nucleotide) accession2taxid file (
--accession2taxid) - (optional) custom seqid2taxid file (
--nucl2taxid)
- taxonomy name dump file (
- krakenuniq
- taxonomy name dump file (
--namesdmp) - taxonomy nodes dump file (
--nodesdmp) - (nucleotide) accession2taxid file (
--accession2taxid)
- taxonomy name dump file (
- malt
- a MEGAN ‘mapDB’ mapping file (
--malt_mapdb)
- a MEGAN ‘mapDB’ mapping file (
What should an X auxiliary file look like?
Some database building tools require additional files to be supplied to the pipeline. These are typically taxonomy files, and each are formatted in different ways.
names dump
This is a NCBI taxdump-style taxonomy file, that associates taxon IDs with human-readable names.
Always refer to the NCBI taxdump README for the most up-to-date information.
It is formatted as a tab-pipe (\t|\t)-separated file with four columns but no header row.
| Column | Column Name* | Description |
|---|---|---|
| 1 | tax_id | The taxon ID |
| 2 | name_txt | The human-readable name of the taxon |
| 3 | unique name | The unique variant of the name if not unique |
| 4 | name class | The type or category of the name (e.g. scientific, common name, synonym) |
* Column names as defined in the taxdump README, however not used in the file itself
Example:
1 | all | | synonym |
1 | root | | scientific name |
2 | Bacteria | Bacteria <bacteria> | scientific name |
2 | bacteria | | blast name |
2 | eubacteria | | genbank common name |
2 | Monera | Monera <bacteria> | in-part |
2 | Procaryotae | Procaryotae <bacteria> | in-part |
2 | Prokaryotae | Prokaryotae <bacteria> | in-part |
2 | Prokaryota | Prokaryota <bacteria> | in-part |
2 | prokaryote | prokaryote <bacteria> | in-part |
2 | prokaryotes | prokaryotes <bacteria> | in-part |
712 | Pasteurellaceae Pohl 1981 | | authority |
712 | Pasteurellaceae | | scientific name |
724 | Haemophilus | | scientific name |
724 | Haemophilus Winslow et al. 1917 | | authority |nodes dump
This is a NCBI taxdump-style taxonomy file, that associates taxon IDs their taxonomic parent within the taxonomic hierarchy.
Always refer to the NCBI taxdump README for the most up-to-date information.
It is formatted as a tab-pipe (\t|\t)-separated file with fourteen columns but no header row.
| Column | Column Name* | Description |
|---|---|---|
| 1 | tax_id | The taxon ID |
| 2 | parent tax_id | The taxon ID of the parent taxon |
| 3 | rank | The NCBI taxonomic rank of the taxon |
| 4 | embl code | The EMBL code for the taxon |
| 5 | division id | The NCBI division ID for the taxon (referring to diversion.dmp NCBI taxdump file not used in nf-core/createtaxdb) |
| 6 | inherited div flag | 1 (true) or 0 flag if taxon entry inherits division ID from taxonomic parent |
| 7 | genetic code id | The genetic code ID for the taxon (referring to gencode.dmp NCBI taxdump file not used in nf-core/createtaxdb) |
| 8 | inherited gc flag | 1 (true) or 0 flag if taxon entry inherits genetic code ID from taxonomic parent |
| 9 | mitochondrial genetic code | The mitochondrial genetic code ID for the taxon (referring to gencode.dmp NCBI taxdump file not used in nf-core/createtaxdb) |
| 10 | inherited mgc flag | 1 (true) or 0 flag if taxonomic entry inherits mitocondrial gencode from parent taxon |
| 11 | genbank hidden flag | 1 (true) or 0 flag indicating if name is suppressed in NCBI GenBank database |
| 13 | hidden subtree root flag node | 1 (true) or 0 flag indicating if there is any sequence data |
| 14 | comments | Comments about the taxon |
* Column names as defined in the taxdump README, however not used in the file itself
Example:
1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | |
712 | 135625 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
724 | 712 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
727 | 724 | species | HI | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified |
815 | 171549 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
816 | 815 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
817 | 816 | species | BF | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified |
976 | 68336 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
1239 | 1783272 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |
1300 | 186826 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
1301 | 1300 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant |
1311 | 1301 | species | SA | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified |accession2taxid
An accession2taxid file is a file that maps database sequence accession IDs (e.g. NCBI GenBank) to their corresponding taxon IDs.
It is formatted as a four column tab-separated file with a header row.
| Column | Column Name | Description |
|---|---|---|
| 1 | accession | The accession ID of the sequence without a version - typically embedded as first part of a FASTA header entry (e.g. for >NC_012920 Homo sapiens mitochondrion, complete genome) the accession is NC_012829) |
| 2 | accesion.version | The full accession version of the accession with the version suffix (e.g. .1) |
| 3 | taxid | The taxon ID corresponding to the names/nodes.dmp |
| 4 | gi | The old-style (now deprecated) NCBI GenInfo Identifier |
Example:
accession accession.version taxid gi
NC_018507 CP003708.1 91844 401871806
NZ_CP019811 CP019811.1 1311 1328913993
NZ_CP069563 CP069563.1 817 1986148684
NZ_CP069564 CP069564.1 817 1986152744
NC_012920 J01415.2 9606 113200490
NZ_LS483480 LS483480.1 727 1403648431
MT192765 MT192765.1 694009 1821109001It’s important to note that you can have multiple accession numbers within a FASTA file (i.e., one per sequence in the file), therefore accession2taxid mapping files should ensure they reference all accession numbers that are present in the FASTA file.
The accession column should not include the accession version in the first column (i.e. 1)
nucl2taxid
An accession2taxid file is a file that maps database sequence accession IDs (e.g. NCBI GenBank) to their corresponding taxon IDs.
It is a simpler version of the accession2taxid file, and is formatted as a two column tab-separated file without a header row.
| Column | Column Name | Description |
|---|---|---|
| 1 | accession | The nucleotide accession ID with version of the sequence - typically embedded as first part of a FASTA header entry (e.g. for >NC_012920.1 Homo sapiens mitochondrion, complete genome) the accession is NC_012829.1) |
| 2 | taxon id | The corresponding taxonmy ID of the sequence |
Example:
NC_012920.1 9606
MT192765.1 694009
NZ_CP069563.1 817
NC_018507.1 91844
NZ_CP019811 1311
NZ_LS483480.1 727
prot2taxid
An accession2taxid file is a file that maps database sequence accession IDs (e.g. NCBI GenBank) to their corresponding taxon IDs.
It is a simpler version of the accession2taxid file, and is formatted as a two column tab-separated file with a header row.
| Column | Column Name | Description |
|---|---|---|
| 1 | accession.version | The protein accession ID with version of the sequence - typically embedded as first part of a FASTA header entry (e.g. for >NC_012920.1 Homo sapiens mitochondrion, complete genome) the accession is NC_012829.1) |
| 2 | taxid | The corresponding taxonmy ID of the sequence |
Example:
accession.version taxid
QIK50426.1 694009
QIK50427.1 694009
QIK50428.1 694009
QIK50429.1 694009
QIK50430.1 694009
QIK50431.1 694009
QIK50432.1 694009
QIK50433.1 694009
QIK50434.1 694009
QIK50435.1 694009
QIK50436.1 694009
WP_000002661.1 1311
WP_000002812.1 1311
WP_000003859.1 1311malt mapDB
A custom taxonomy database file from the MEGAN6 toolkit ending with .db.
This file must be unzipped before use, and is an SQLlite database consisting of two tables
info- Three column table:
id.info_string,size - Two rows:
general,Taxonomy - The
info_stringofgeneralhas a string of Created- - : : , and a size of the number of taxonomic entries in the database - The
info_stringofTaxonomyhas a string ofSource: nucl_gb.accession2taxid.gzand a size of taxonomic entries in the database
- Three column table:
mappings- A two column table:
Accession,Taxonomy - The
Accessioncolumn contains the accession ID of the sequence with version (e.g.NC_012920.1)
- A two column table:
I want to supply a custom seqid2taxid file to kraken2
While not officially supported by Kraken2, you can speed up the Kraken2 build process by providing the pipeline a premade seqid2taxid.map file.
This file should be a tab-separated file with two columns:
- the sequence ID as represented by the first part of each
>entry of a FASTA file - the taxon ID
To supply this to the pipeline, you can give this to the --nucl2taxid parameter, as the Kraken2 seqid2taxid.map file is the same as Centrifuge’s --conversion-table file.