A python package with helper tools for the nf-core community.
- Installation
- Listing pipelines (
nf-core list) - Downloading pipelines for offline use (
nf-core download) - Listing software licences: List software licences for a given workflow (
nf-core licences) - Creating a new workflow (
nf-core create) - Checking a pipeline against nf-core guidelines (
nf-core lint) - Bumping a pipeline version number (
nf-core bump-version)
You can install nf-core/tools from PyPI using pip as follows:
pip install nf-core
If you would like the development version instead, the command is:
pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
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 the package
python setup.py develop
# Alternatively, install with pip
pip install -e .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
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Name Version Published Last Pulled Default local is latest release?
----------------- --------- ----------- ------------- ----------------------------------
nf-core/hlatyping 1.1.0 5 days ago 9 minutes ago Yes
nf-core/methylseq 1.1 1 week ago 2 months ago No
nf-core/chipseq dev - - No
nf-core/eager dev - - No
nf-core/exoseq dev - - No
nf-core/mag dev - - No
nf-core/rnaseq dev - - No
nf-core/smrnaseq dev - - No
nf-core/vipr dev - - No
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
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Name Version Published Last Pulled Default local is latest release?
---------------- --------- ------------ ------------- ----------------------------------
nf-core/rnaseq 1.0 20 hours ago - No
nf-core/smrnaseq dev - - No
You can sort the results by latest release (default), name (alphabetical) or number of GitHub stars using the -s/--stars option.
Finally, to return machine-readable JSON output, use the --json flag.
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 just download the pipeline code. If you specify the flag --singularity, it will also download any singularity image files that are required.
$ nf-core download methylseq --singularity
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INFO: Saving methylseq
Pipeline release: 1.0
Pull singularity containers: Yes
Output directory: nf-core-methylseq-1.0
INFO: Downloading workflow files from GitHub
INFO: Downloading 1 singularity container
nf-core-methylseq-1.0.simg [762.28MB] [####################################] 780573/780572
$ tree -L 2 nf-core-methylseq-1.0/
nf-core-methylseq-1.0/
├── singularity-images
│ └── nf-core-methylseq-1.0.simg
└── workflow
├── CHANGELOG.md
├── Dockerfile
├── LICENCE.md
├── README.md
├── assets
├── bin
├── conf
├── docs
├── environment.yml
├── main.nf
├── nextflow.config
└── tests
7 directories, 8 files
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
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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
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
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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 masterYou 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.
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 .
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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.
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
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INFO: Running nf-core lint tests
Running pipeline tests [####################################] 100% None
INFO: ===========
LINTING RESULTS
=================
96 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
- container = 'nfcore/mypipeline:latest'
+ container = 'nfcore/mypipeline:1.0'
INFO: Updating version in .travis.yml
- docker tag nfcore/mypipeline nfcore/mypipeline:latest
+ docker tag nfcore/mypipeline nfcore/mypipeline:1.0
INFO: Updating version in Singularity
- VERSION 1.0dev
+ VERSION 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
- PATH /opt/conda/envs/nf-core-mypipeline-1.0dev/bin:$PATH
+ PATH /opt/conda/envs/nf-core-mypipeline-1.0/bin:\$PATH
INFO: Updating version in Singularity
- PATH=/opt/conda/envs/nf-core-mypipeline-1.0dev/bin:$PATH
+ PATH=/opt/conda/envs/nf-core-mypipeline-1.0/bin:\$PATH
To change the required version of Nextflow instead of the pipeline version number, use the flag --nextflow.