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nf-core/tools

Python tests codecov install with Bioconda install with PyPI Get help on Slack

A python package with helper tools for the nf-core community.

Read this documentation on the nf-core website: https://nf-co.re/tools

Table of contents

The nf-core tools package is written in Python and can be imported and used within other packages. For documentation of the internal Python functions, please refer to the Tools Python API docs.

Installation

Bioconda

You can install nf-core/tools from bioconda.

First, install conda and configure the channels to use bioconda (see the bioconda documentation). Then, just run the conda installation command:

conda install nf-core

Alternatively, you can create a new environment with both nf-core/tools and nextflow:

conda create --name nf-core python=3.7 nf-core nextflow
conda activate nf-core

Python Package Index

nf-core/tools can also be installed from PyPI using pip as follows:

pip install nf-core

Development version

If you would like the latest development version of tools, the command is:

pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev

If you intend to make edits to the code, first make a fork of the repository and then clone it locally. Go to the cloned directory and either install with pip:

pip install -e .

Or install directly using Python:

python setup.py develop

Listing pipelines

The command nf-core list shows all available nf-core pipelines along with their latest version, when that was published and how recently the pipeline code was pulled to your local system (if at all).

An example of the output from the command is as follows:

$ nf-core list

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


Name                       Version    Released      Last Pulled     Have latest release?
-------------------------  ---------  ------------  --------------  ----------------------
nf-core/rnaseq             1.3        4 days ago    27 minutes ago  Yes
nf-core/hlatyping          1.1.4      3 weeks ago   1 months ago    No
nf-core/eager              2.0.6      3 weeks ago   -               -
nf-core/mhcquant           1.2.6      3 weeks ago   -               -
nf-core/rnafusion          1.0        1 months ago  -               -
nf-core/methylseq          1.3        1 months ago  3 months ago    No
nf-core/ampliseq           1.0.0      3 months ago  -               -
nf-core/deepvariant        1.0        4 months ago  -               -
nf-core/atacseq            dev        -             1 months ago    No
nf-core/bacass             dev        -             -               -
nf-core/bcellmagic         dev        -             -               -
nf-core/chipseq            dev        -             1 months ago    No
nf-core/clinvap            dev        -             -               -

To narrow down the list, supply one or more additional keywords to filter the pipelines based on matches in titles, descriptions and topics:

$ nf-core list rna rna-seq

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


Name               Version    Released      Last Pulled     Have latest release?
-----------------  ---------  ------------  --------------  ----------------------
nf-core/rnaseq     1.3        4 days ago    28 minutes ago  Yes
nf-core/rnafusion  1.0        1 months ago  -               -
nf-core/lncpipe    dev        -             -               -
nf-core/smrnaseq   dev        -             -               -

You can sort the results by latest release (-s release, default), when you last pulled a local copy (-s pulled), alphabetically (-s name), or number of GitHub stars (-s stars).

$ nf-core list -s stars

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


Name                         Stargazers  Version    Released      Last Pulled     Have latest release?
-------------------------  ------------  ---------  ------------  --------------  ----------------------
nf-core/rnaseq                       81  1.3        4 days ago    30 minutes ago  Yes
nf-core/methylseq                    22  1.3        1 months ago  3 months ago    No
nf-core/ampliseq                     21  1.0.0      3 months ago  -               -
nf-core/chipseq                      20  dev        -             1 months ago    No
nf-core/deepvariant                  15  1.0        4 months ago  -               -
nf-core/eager                        14  2.0.6      3 weeks ago   -               -
nf-core/rnafusion                    14  1.0        1 months ago  -               -
nf-core/lncpipe                       9  dev        -             -               -
nf-core/exoseq                        8  dev        -             -               -
nf-core/mag                           8  dev        -             -               -

Finally, to return machine-readable JSON output, use the --json flag.

Launch a pipeline

Some nextflow pipelines have a considerable number of command line flags that can be used. To help with this, the nf-core launch command uses an interactive command-line wizard tool to prompt you for values for running nextflow and the pipeline parameters.

The tool uses the nextflow_schema.json file from a pipeline to give parameter descriptions, defaults and grouping. If no file for the pipeline is found, one will be automatically generated at runtime.

Nextflow params variables are saved in to a JSON file called nf-params.json and used by nextflow with the -params-file flag. This makes it easier to reuse these in the future.

The nf-core launch command is an interactive command line tool and prompts you to overwrite the default values for each parameter. Entering ? for any parameter will give a full description from the documentation of what that value does.

$ nf-core launch rnaseq

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 1.10.dev0


INFO: [✓] Pipeline schema looks valid

INFO: This tool ignores any pipeline parameter defaults overwritten by Nextflow config files or profiles

? Nextflow command-line flags  (Use arrow keys)
 ❯ Continue >>
   ---------------
   -name
   -revision
   -profile
   -work-dir
   -resume

Once complete, the wizard will ask you if you want to launch the Nextflow run. If not, you can copy and paste the Nextflow command with the nf-params.json file of your inputs.

? Nextflow command-line flags  Continue >>
? Input/output options  input

Input FastQ files. (? for help)
? input  data/*{1,2}.fq.gz
? Input/output options  Continue >>
? Reference genome options  Continue >>

INFO: [✓] Input parameters look valid

INFO: Nextflow command:
  nextflow run nf-core-testpipeline/ -params-file "nf-params.json"


Do you want to run this command now? [y/N]: n

Launch tool options

  • -c, --command-only
    • If you prefer not to save your inputs in a JSON file and use -params-file, this option will specify all entered params directly in the nextflow command.
  • -p, --params-in PATH
    • To use values entered in a previous pipeline run, you can supply the nf-params.json file previously generated.
    • This will overwrite the pipeline schema defaults before the wizard is launched.
  • -o, --params-out PATH
    • Path to save parameters JSON file to. (Default: nf-params.json)
  • -a, --save-all
    • Without this option the pipeline will ignore any values that match the pipeline schema defaults.
    • This option saves all parameters found to the JSON file.
  • -h, --show-hidden
    • A pipeline JSON schema can define some parameters as 'hidden' if they are rarely used or for internal pipeline use only.
    • This option forces the wizard to show all parameters, including those labelled as 'hidden'.

Downloading pipelines for offline use

Sometimes you may need to run an nf-core pipeline on a server or HPC system that has no internet connection. In this case you will need to fetch the pipeline files first, then manually transfer them to your system.

To make this process easier and ensure accurate retrieval of correctly versioned code and software containers, we have written a download helper tool. Simply specify the name of the nf-core pipeline and it will be downloaded to your current working directory.

By default, the pipeline will download the pipeline code and the institutional nf-core/configs files. If you specify the flag --singularity, it will also download any singularity image files that are required.

Use -r/--release to download a specific release of the pipeline. If not specified, the tool will automatically fetch the latest release.

$ nf-core download methylseq -r 1.4 --singularity

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Saving methylseq
 Pipeline release: 1.4
 Pull singularity containers: Yes
 Output file: nf-core-methylseq-1.4.tar.gz

INFO: Downloading workflow files from GitHub

INFO: Downloading centralised configs from GitHub

INFO: Downloading 1 singularity container

INFO: Building singularity image from Docker Hub: docker://nfcore/methylseq:1.4
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
....
INFO:    Creating SIF file...
INFO:    Build complete: /my-pipelines/nf-core-methylseq-1.4/singularity-images/nf-core-methylseq-1.4.simg

INFO: Compressing download..

INFO: Command to extract files: tar -xzf nf-core-methylseq-1.4.tar.gz

INFO: MD5 checksum for nf-core-methylseq-1.4.tar.gz: f5c2b035619967bb227230bc3ec986c5

The tool automatically compresses all of the resulting file in to a .tar.gz archive. You can choose other formats (.tar.bz2, zip) or to not compress (none) with the -c/--compress flag. The console output provides the command you need to extract the files.

Once uncompressed, you will see the following file structure for the downloaded pipeline:

$ tree -L 2 nf-core-methylseq-1.4/

nf-core-methylseq-1.4
├── configs
│   ├── bin
│   ├── conf
│   ├── configtest.nf
│   ├── docs
│   ├── LICENSE
│   ├── nextflow.config
│   ├── nfcore_custom.config
│   └── README.md
├── singularity-images
│   └── nf-core-methylseq-1.4.simg
└── workflow
    ├── assets
    ├── bin
    ├── CHANGELOG.md
    ├── CODE_OF_CONDUCT.md
    ├── conf
    ├── Dockerfile
    ├── docs
    ├── environment.yml
    ├── LICENSE
    ├── main.nf
    ├── nextflow.config
    ├── nextflow_schema.json
    └── README.md

10 directories, 15 files

The pipeline files are automatically updated so that the local copy of institutional configs are available when running the pipeline. So using -profile <NAME> should work if available within nf-core/configs.

You can run the pipeline by simply providing the directory path for the workflow folder. Note that if using Singularity, you will also need to provide the path to the Singularity image. For example:

nextflow run /path/to/nf-core-methylseq-1.4/workflow/ \
     -profile singularity \
     -with-singularity /path/to/nf-core-methylseq-1.4/singularity-images/nf-core-methylseq-1.4.simg \
     # .. other normal pipeline parameters from here on..
     --input '*_R{1,2}.fastq.gz' --genome GRCh38

Pipeline software licences

Sometimes it's useful to see the software licences of the tools used in a pipeline. You can use the licences subcommand to fetch and print the software licence from each conda / PyPI package used in an nf-core pipeline.

$ nf-core licences rnaseq

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Warning: This tool only prints licence information for the software tools packaged using conda.
        The pipeline may use other software and dependencies not described here.

Package Name           Version    Licence
---------------------  ---------  --------------------
stringtie              1.3.3      Artistic License 2.0
preseq                 2.0.3      GPL
trim-galore            0.4.5      GPL
bioconductor-edger     3.20.7     GPL >=2
fastqc                 0.11.7     GPL >=3
openjdk                8.0.144    GPLv2
r-gplots               3.0.1      GPLv2
r-markdown             0.8        GPLv2
rseqc                  2.6.4      GPLv2
bioconductor-dupradar  1.8.0      GPLv3
hisat2                 2.1.0      GPLv3
multiqc                1.5        GPLv3
r-data.table           1.10.4     GPLv3
star                   2.5.4a     GPLv3
subread                1.6.1      GPLv3
picard                 2.18.2     MIT
samtools               1.8        MIT

Creating a new workflow

The create subcommand makes a new workflow using the nf-core base template. With a given pipeline name, description and author, it makes a starter pipeline which follows nf-core best practices.

After creating the files, the command initialises the folder as a git repository and makes an initial commit. This first "vanilla" commit which is identical to the output from the templating tool is important, as it allows us to keep your pipeline in sync with the base template in the future. See the nf-core syncing docs for more information.

$ nf-core create

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

Workflow Name: nextbigthing
Description: This pipeline analyses data from the next big 'omics technique
Author: Big Steve

INFO: Creating new nf-core pipeline: nf-core/nextbigthing

INFO: Initialising pipeline git repository

INFO: Done. Remember to add a remote and push to GitHub:
  cd /path/to/nf-core-nextbigthing
  git remote add origin git@github.com:USERNAME/REPO_NAME.git
  git push --all origin

INFO: This will also push your newly created dev branch and the TEMPLATE branch for syncing.

INFO: !!!!!! IMPORTANT !!!!!!

If you are interested in adding your pipeline to the nf-core community,
PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE!

Please read: https://nf-co.re/developers/adding_pipelines#join-the-community

Once you have run the command, create a new empty repository on GitHub under your username (not the nf-core organisation, yet) and push the commits from your computer using the example commands in the above log. You can then continue to edit, commit and push normally as you build your pipeline.

Please see the nf-core documentation for a full walkthrough of how to create a new nf-core workflow.

Note that if the required arguments for nf-core create are not given, it will interactively prompt for them. If you prefer, you can supply them as command line arguments. See nf-core create --help for more information.

Linting a workflow

The lint subcommand checks a given pipeline for all nf-core community guidelines. This is the same test that is used on the automated continuous integration tests.

For example, the current version looks something like this:

$ cd path/to/my_pipeline
$ nf-core lint .

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

Running pipeline tests  [####################################]  100%  None

INFO: ===========
 LINTING RESULTS
=================
  72 tests passed   2 tests had warnings   0 tests failed

WARNING: Test Warnings:
  https://nf-co.re/errors#8: Conda package is not latest available: picard=2.18.2, 2.18.6 available
  https://nf-co.re/errors#8: Conda package is not latest available: bwameth=0.2.0, 0.2.1 available

You can find extensive documentation about each of the lint tests in the lint errors documentation.

Working with pipeline schema

nf-core pipelines have a nextflow_schema.json file in their root which describes the different parameters used by the workflow. These files allow automated validation of inputs when running the pipeline, are used to generate command line help and can be used to build interfaces to launch pipelines. Pipeline schema files are built according to the JSONSchema specification (Draft 7).

To help developers working with pipeline schema, nf-core tools has three schema sub-commands:

  • nf-core schema validate
  • nf-core schema build
  • nf-core schema lint

nf-core schema validate

Nextflow can take input parameters in a JSON or YAML file when running a pipeline using the -params-file option. This command validates such a file against the pipeline schema.

Usage is nextflow schema validate <pipeline> --params <parameter file>, eg:

$ nf-core schema validate my_pipeline --params my_inputs.json

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: [✓] Pipeline schema looks valid

ERROR: [✗] Input parameters are invalid: 'input' is a required property

The pipeline option can be a directory containing a pipeline, a path to a schema file or the name of an nf-core pipeline (which will be downloaded using nextflow pull).

nf-core schema build

Manually building JSONSchema documents is not trivial and can be very error prone. Instead, the nf-core schema build command collects your pipeline parameters and gives interactive prompts about any missing or unexpected params. If no existing schema is found it will create one for you.

Once built, the tool can send the schema to the nf-core website so that you can use a graphical interface to organise and fill in the schema. The tool checks the status of your schema on the website and once complete, saves your changes locally.

Usage is nextflow schema build <pipeline_directory>, eg:

$ nf-core schema build nf-core-testpipeline

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Loaded existing JSON schema with 18 params: nf-core-testpipeline/nextflow_schema.json

Unrecognised 'params.old_param' found in schema but not in Nextflow config. Remove it? [Y/n]:
Unrecognised 'params.we_removed_this_too' found in schema but not in Nextflow config. Remove it? [Y/n]:

INFO: Removed 2 params from existing JSON Schema that were not found with `nextflow config`:
 old_param, we_removed_this_too

Found 'params.input' in Nextflow config. Add to JSON Schema? [Y/n]:
Found 'params.outdir' in Nextflow config. Add to JSON Schema? [Y/n]:

INFO: Added 2 params to JSON Schema that were found with `nextflow config`:
 input, outdir

INFO: Writing JSON schema with 18 params: nf-core-testpipeline/nextflow_schema.json

Launch web builder for customisation and editing? [Y/n]:

INFO: Opening URL: http://localhost:8888/json_schema_build?id=1584441828_b990ac785cd6

INFO: Waiting for form to be completed in the browser. Use ctrl+c to stop waiting and force exit.
..........
INFO: Found saved status from nf-core JSON Schema builder

INFO: Writing JSON schema with 18 params: nf-core-testpipeline/nextflow_schema.json

There are three flags that you can use with this command:

  • --no-prompts: Make changes without prompting for confirmation each time. Does not launch web tool.
  • --web-only: Skips comparison of the schema against the pipeline parameters and only launches the web tool.
  • --url <web_address>: Supply a custom URL for the online tool. Useful when testing locally.

nf-core schema lint

The pipeline schema is linted as part of the main nf-core lint command, however sometimes it can be useful to quickly check the syntax of the JSONSchema without running a full lint run.

Usage is nextflow schema lint <schema>, eg:

$ nf-core schema lint nextflow_schema.json

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


ERROR: [✗] JSON Schema does not follow nf-core specs:
 Schema should have 'properties' section

Bumping a pipeline version number

When releasing a new version of a nf-core pipeline, version numbers have to be updated in several different places. The helper command nf-core bump-version automates this for you to avoid manual errors (and frustration!).

The command uses results from the linting process, so will only work with workflows that pass these tests.

Usage is nf-core bump-version <pipeline_dir> <new_version>, eg:

$ cd path/to/my_pipeline
$ nf-core bump-version . 1.0

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Running nf-core lint tests
Running pipeline tests  [####################################]  100%  None

INFO: ===========
 LINTING RESULTS
=================
  118 tests passed   0 tests had warnings   0 tests failed

INFO: Changing version number:
  Current version number is '1.0dev'
  New version number will be '1.0'

INFO: Updating version in nextflow.config
 - version = '1.0dev'
 + version = '1.0'

INFO: Updating version in nextflow.config
 - process.container = 'nfcore/mypipeline:dev'
 + process.container = 'nfcore/mypipeline:1.0'

INFO: Updating version in .github/workflows/ci.yml
 - docker tag nfcore/mypipeline:dev nfcore/mypipeline:dev
 + docker tag nfcore/mypipeline:dev nfcore/mypipeline:1.0

INFO: Updating version in environment.yml
 - name: nf-core-mypipeline-1.0dev
 + name: nf-core-mypipeline-1.0

INFO: Updating version in Dockerfile
 - ENV PATH /opt/conda/envs/nf-core-mypipeline-1.0dev/bin:$PATH
 - RUN conda env export --name nf-core-mypipeline-1.0dev > nf-core-mypipeline-1.0dev.yml
 + ENV PATH /opt/conda/envs/nf-core-mypipeline-1.0/bin:$PATH
 + RUN conda env export --name nf-core-mypipeline-1.0 > nf-core-mypipeline-1.0.yml

To change the required version of Nextflow instead of the pipeline version number, use the flag --nextflow.

To export the lint results to a JSON file, use --json [filename]. For markdown, use --markdown [filename].

As linting tests can give a pass state for CI but with warnings that need some effort to track down, the linting code attempts to post a comment to the GitHub pull-request with a summary of results if possible. It does this when the environment variables GITHUB_COMMENTS_URL and GITHUB_TOKEN are set and if there are any failing or warning tests. If a pull-request is updated with new commits, the original comment will be updated with the latest results instead of posting lots of new comments for each git push.

A typical GitHub Actions step with the required environment variables may look like this (will only work on pull-request events):

- name: Run nf-core lint
  env:
    GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
    GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
  run: nf-core lint $GITHUB_WORKSPACE

Sync a pipeline with the template

Over time, the main nf-core pipeline template is updated. To keep all nf-core pipelines up to date, we synchronise these updates automatically when new versions of nf-core/tools are released. This is done by maintaining a special TEMPLATE branch, containing a vanilla copy of the nf-core template with only the variables used when it first ran (name, description etc.). This branch is updated and a pull-request can be made with just the updates from the main template code.

This command takes a pipeline directory and attempts to run this synchronisation. Usage is nf-core sync <pipeline_dir>, eg:

$ nf-core sync my_pipeline/

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Pipeline directory: /path/to/my_pipeline

INFO: Fetching workflow config variables

INFO: Deleting all files in TEMPLATE branch

INFO: Making a new template pipeline using pipeline variables

INFO: Committed changes to TEMPLATE branch

INFO: Now try to merge the updates in to your pipeline:
  cd /path/to/my_pipeline
  git merge TEMPLATE

If your pipeline repository does not already have a TEMPLATE branch, you can instruct the command to try to create one by giving the --make-template-branch flag. If it has to, the sync tool will then create an orphan branch - see the nf-core website sync documentation for details on how to handle this.

By default, the tool will collect workflow variables from the current branch in your pipeline directory. You can supply the --from-branch flag to specific a different branch.

Finally, if you give the --pull-request flag, the command will push any changes to the remote and attempt to create a pull request using the GitHub API. The GitHub username and repository name will be fetched from the remote url (see git remote -v | grep origin), or can be supplied with --username and --repository.

To create the pull request, a personal access token is required for API authentication. These can be created at https://github.com/settings/tokens. Supply this using the --auth-token flag.

Finally, if --all is supplied, then the command attempts to pull and synchronise all nf-core workflows. This is used by the nf-core/tools release automation to synchronise all nf-core pipelines with the newest version of the template. It requires authentication as either the nf-core-bot account or as an nf-core administrator.

$ nf-core sync --all

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Syncing nf-core/ampliseq

[...]

INFO: Successfully synchronised [n] pipelines

Citation

If you use nf-core tools in your work, please cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. ReadCube: Full Access Link

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