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

Table of contents

• nf-core tools installation
• nf-core list - List available pipelines
• nf-core launch - Run a pipeline with interactive parameter prompts
• nf-core download - Download pipeline for offline use
• nf-core licences - List software licences in a pipeline
• nf-core create - Create a new workflow from the nf-core template
• nf-core lint - Check pipeline code against nf-core guidelines
• nf-core bump-version - Update nf-core pipeline version number
• nf-core sync - Synchronise pipeline TEMPLATE branches
• Citation

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

You can install nf-core/tools using bioconda:

conda install -c bioconda nf-core

It can also be installed from PyPI using pip as follows:

pip install nf-core

Or, if you would like the development version instead, the command is:

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

Alternatively, if you would like to edit the files locally: Clone the repository code - you should probably specify your fork instead

git clone https://github.com/nf-core/tools.git nf-core-tools
cd nf-core-tools

Install with pip

pip install -e .

Alternatively, install the package with 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.

If the pipeline in question has a parameters.settings.json file following the nf-core parameter JSON schema, parameters will be grouped and have associated description text and variable typing.

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

It is not essential to run the pipeline - the wizard will ask you if you want to launch the command at the end. If not, you finish with the params JSON file and a nextflow command that you can copy and paste.

$ nf-core launch rnaseq

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


INFO: Launching nf-core/rnaseq
Main nextflow options

Config profile to use
 -profile [standard]: docker

Unique name for this nextflow run
 -name [None]: test_run

Work directory for intermediate files
 -w [./work]:

Resume a previous workflow run
 -resume [y/N]:

Release / revision to use
 -r [None]: 1.3


Parameter group: Main options
Do you want to change the group's defaults? [y/N]: y

Input files
Specify the location of your input FastQ files.
 --reads ['data/*{1,2}.fastq.gz']: '/path/to/reads_*{R1,R2}.fq.gz'

[..truncated..]

Nextflow command:
  nextflow run nf-core/rnaseq -profile "docker" -name "test_run" -r "1.3" -params-file "/Users/ewels/testing/nfx-params.json"


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

INFO: Launching workflow!
N E X T F L O W  ~  version 19.01.0
Launching `nf-core/rnaseq` [evil_engelbart] - revision: 37f260d360 [master]

[..truncated..]

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 dockerhub: 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
    ├── parameters.settings.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..
     --reads '*_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

Once you have run the command, create a new empty repository on GitHub under your username (not the nf-core organisation, yet). On your computer, add this repository as a git remote and push to it:

git remote add origin https://github.com/ewels/nf-core-nextbigthing.git
git push --set-upstream origin master

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:
  http://nf-co.re/errors#8: Conda package is not latest available: picard=2.18.2, 2.18.6 available
  http://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.

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.

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.
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