Helper tools for use with nf-core Nextflow pipelines.
Project description
A python package with helper tools for the nf-core community.
Table of contents
nf-coretools installationnf-core list- List available pipelinesnf-core launch- Run a pipeline with interactive parameter promptsnf-core download- Download pipeline for offline usenf-core licences- List software licences in a pipelinenf-core create- Create a new workflow from the nf-core templatenf-core lint- Check pipeline code against nf-core guidelinesnf-core bump-version- Update nf-core pipeline version number
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 from PyPI using pip as follows:
pip install nf-core
Alternatively, it can be installed using bioconda:
conda install -c bioconda 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 .
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 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 ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' 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
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 ================= 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:dev' + container = 'nfcore/mypipeline:1.0' INFO: Updating version in .travis.yml - docker tag nfcore/mypipeline:dev nfcore/mypipeline:latest + docker tag nfcore/mypipeline:dev 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.
Citation
If you use nf-core tools in your work, please cite the nf-core preprint as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.
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