Metadata-Version: 2.1
Name: nf-core
Version: 1.6
Summary: Helper tools for use with nf-core Nextflow pipelines.
Home-page: https://github.com/nf-core/tools
Author: Phil Ewels
Author-email: phil.ewels@scilifelab.se
License: MIT License

Copyright (c) 2018 nf-core

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Description: # ![nf-core/tools](docs/images/nf-core-logo.png)
        
        ## [nf-core/tools](https://github.com/nf-core/tools)
        [![Build Status](https://travis-ci.org/nf-core/tools.svg?branch=master)](https://travis-ci.org/nf-core/tools)
        [![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/nf-core/README.html)
        
        A python package with helper tools for the nf-core community.
        
        ## Table of contents
        
        * [`nf-core` tools installation](#installation)
        * [`nf-core list` - List available pipelines](#listing-pipelines)
        * [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)
        * [`nf-core download` - Download pipeline for offline use](#downloading-pipelines-for-offline-use)
        * [`nf-core licences` - List software licences in a pipeline](#pipeline-software-licences)
        * [`nf-core create` - Create a new workflow from the nf-core template](#creating-a-new-workflow)
        * [`nf-core lint` - Check pipeline code against nf-core guidelines](#linting-a-workflow)
        * [`nf-core bump-version` - Update nf-core pipeline version number](#bumping-a-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](https://nf-co.re/tools-docs/).
        
        ## Installation
        
        You can install `nf-core/tools` from [PyPI](https://pypi.python.org/pypi/nf-core/) using pip as follows:
        
        ```bash
        pip install nf-core
        ```
        
        Alternatively, it can be installed using [bioconda](https://bioconda.github.io/recipes/nf-core/README.html):
        
        ```bash
        conda install -c bioconda nf-core
        ```
        
        If you would like the development version instead, the command is:
        
        ```bash
        pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
        ```
        
        Alternatively, if you would like to edit the files locally:
        
        ```bash
        # 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:
        
        ```console
        $ 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:
        
        ```console
        $ 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`).
        
        ```console
        $ 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](https://nf-co.re/parameters.schema.json), 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.
        
        ```console
        $ 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.
        
        ```console
        $ 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
        ```
        
        ```console
        $ 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.
        
        ```console
        $ 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](http://nf-co.re/sync) for more information.
        
        ```console
        $ 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:
        
        ```console
        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](https://nf-co.re/adding_pipelines) 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:
        
        ```console
        $ 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](https://nf-co.re/errors).
        
        
        ## 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:
        
        ```console
        $ 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`.
        
Keywords: nf-core,nextflow,bioinformatics,workflow,pipeline,biology,sequencing,NGS,next generation sequencing
Platform: UNKNOWN
Description-Content-Type: text/markdown
