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        "author": "Phil Ewels",
        "author_email": "phil.ewels@scilifelab.se",
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        "description": "# ![nf-core/tools](docs/images/nfcore-tools_logo.png)\n\n[![Build Status](https://travis-ci.org/nf-core/tools.svg?branch=master)](https://travis-ci.org/nf-core/tools)\n[![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)\n[![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)\n\nA python package with helper tools for the nf-core community.\n\n## Table of contents\n\n* [`nf-core` tools installation](#installation)\n* [`nf-core list` - List available pipelines](#listing-pipelines)\n* [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)\n* [`nf-core download` - Download pipeline for offline use](#downloading-pipelines-for-offline-use)\n* [`nf-core licences` - List software licences in a pipeline](#pipeline-software-licences)\n* [`nf-core create` - Create a new workflow from the nf-core template](#creating-a-new-workflow)\n* [`nf-core lint` - Check pipeline code against nf-core guidelines](#linting-a-workflow)\n* [`nf-core bump-version` - Update nf-core pipeline version number](#bumping-a-pipeline-version-number)\n\n\nThe nf-core tools package is written in Python and can be imported and used within other packages.\nFor documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools-docs/).\n\n## Installation\n\nYou can install `nf-core/tools` from [PyPI](https://pypi.python.org/pypi/nf-core/) using pip as follows:\n\n```bash\npip install nf-core\n```\n\nAlternatively, it can be installed using [bioconda](https://bioconda.github.io/recipes/nf-core/README.html):\n\n```bash\nconda install -c bioconda nf-core\n```\n\nIf you would like the development version instead, the command is:\n\n```bash\npip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git\n```\n\nAlternatively, if you would like to edit the files locally:\n\n```bash\n# Clone the repository code - you should probably specify your fork instead\ngit clone https://github.com/nf-core/tools.git nf-core-tools\ncd nf-core-tools\n\n# Install the package\npython setup.py develop\n\n# Alternatively, install with pip\npip install -e .\n```\n\n## Listing pipelines\nThe 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).\n\nAn example of the output from the command is as follows:\n\n```console\n$ nf-core list\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nName                       Version    Released      Last Pulled     Have latest release?\n-------------------------  ---------  ------------  --------------  ----------------------\nnf-core/rnaseq             1.3        4 days ago    27 minutes ago  Yes\nnf-core/hlatyping          1.1.4      3 weeks ago   1 months ago    No\nnf-core/eager              2.0.6      3 weeks ago   -               -\nnf-core/mhcquant           1.2.6      3 weeks ago   -               -\nnf-core/rnafusion          1.0        1 months ago  -               -\nnf-core/methylseq          1.3        1 months ago  3 months ago    No\nnf-core/ampliseq           1.0.0      3 months ago  -               -\nnf-core/deepvariant        1.0        4 months ago  -               -\nnf-core/atacseq            dev        -             1 months ago    No\nnf-core/bacass             dev        -             -               -\nnf-core/bcellmagic         dev        -             -               -\nnf-core/chipseq            dev        -             1 months ago    No\nnf-core/clinvap            dev        -             -               -\n```\n\nTo narrow down the list, supply one or more additional keywords to filter the pipelines based on matches in titles, descriptions and topics:\n\n```console\n$ nf-core list rna rna-seq\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nName               Version    Released      Last Pulled     Have latest release?\n-----------------  ---------  ------------  --------------  ----------------------\nnf-core/rnaseq     1.3        4 days ago    28 minutes ago  Yes\nnf-core/rnafusion  1.0        1 months ago  -               -\nnf-core/lncpipe    dev        -             -               -\nnf-core/smrnaseq   dev        -             -               -\n```\n\nYou can sort the results by latest release (`-s release`, default),\nwhen you last pulled a local copy (`-s pulled`),\nalphabetically (`-s name`),\nor number of GitHub stars (`-s stars`).\n\n```console\n$ nf-core list -s stars\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nName                         Stargazers  Version    Released      Last Pulled     Have latest release?\n-------------------------  ------------  ---------  ------------  --------------  ----------------------\nnf-core/rnaseq                       81  1.3        4 days ago    30 minutes ago  Yes\nnf-core/methylseq                    22  1.3        1 months ago  3 months ago    No\nnf-core/ampliseq                     21  1.0.0      3 months ago  -               -\nnf-core/chipseq                      20  dev        -             1 months ago    No\nnf-core/deepvariant                  15  1.0        4 months ago  -               -\nnf-core/eager                        14  2.0.6      3 weeks ago   -               -\nnf-core/rnafusion                    14  1.0        1 months ago  -               -\nnf-core/lncpipe                       9  dev        -             -               -\nnf-core/exoseq                        8  dev        -             -               -\nnf-core/mag                           8  dev        -             -               -\n```\n\nFinally, to return machine-readable JSON output, use the `--json` flag.\n\n## Launch a pipeline\nSome nextflow pipelines have a considerable number of command line flags that can be used.\nTo help with this, the `nf-core launch` command uses an interactive command-line wizard tool to prompt you for\nvalues for running nextflow and the pipeline parameters.\n\nIf the pipeline in question has a `parameters.settings.json` file following the [nf-core parameter JSON schema](https://nf-co.re/parameter-schema), parameters will be grouped and have associated description text and variable typing.\n\nNextflow `params` variables are saved in to a JSON file called `nfx-params.json` and used by nextflow with the `-params-file` flag.\nThis makes it easier to reuse these in the future.\n\nIt is not essential to run the pipeline - the wizard will ask you if you want to launch the command at the end.\nIf not, you finish with the `params` JSON file and a nextflow command that you can copy and paste.\n\n```console\n$ nf-core launch rnaseq\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nINFO: Launching nf-core/rnaseq\nMain nextflow options\n\nConfig profile to use\n -profile [standard]: docker\n\nUnique name for this nextflow run\n -name [None]: test_run\n\nWork directory for intermediate files\n -w [./work]:\n\nResume a previous workflow run\n -resume [y/N]:\n\nRelease / revision to use\n -r [None]: 1.3\n\n\nParameter group: Main options\nDo you want to change the group's defaults? [y/N]: y\n\nInput files\nSpecify the location of your input FastQ files.\n --reads ['data/*{1,2}.fastq.gz']: '/path/to/reads_*{R1,R2}.fq.gz'\n\n[..truncated..]\n\nNextflow command:\n  nextflow run nf-core/rnaseq -profile \"docker\" -name \"test_run\" -r \"1.3\" --params-file \"/Users/ewels/testing/nfx-params.json\"\n\n\nDo you want to run this command now? [y/N]: y\n\nINFO: Launching workflow!\nN E X T F L O W  ~  version 19.01.0\nLaunching `nf-core/rnaseq` [evil_engelbart] - revision: 37f260d360 [master]\n\n[..truncated..]\n```\n\n\n## Downloading pipelines for offline use\nSometimes 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.\n\nTo 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.\n\nBy 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.\n\n```console\n$ nf-core download methylseq --singularity\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nINFO: Saving methylseq\n Pipeline release: 1.0\n Pull singularity containers: Yes\n Output directory: nf-core-methylseq-1.0\n\nINFO: Downloading workflow files from GitHub\n\nINFO: Downloading 1 singularity container\nnf-core-methylseq-1.0.simg [762.28MB]  [####################################]  780573/780572\n```\n\n```console\n$ tree -L 2 nf-core-methylseq-1.0/\n\nnf-core-methylseq-1.0/\n\u251c\u2500\u2500 singularity-images\n\u2502\u00a0\u00a0 \u2514\u2500\u2500 nf-core-methylseq-1.0.simg\n\u2514\u2500\u2500 workflow\n    \u251c\u2500\u2500 CHANGELOG.md\n    \u251c\u2500\u2500 Dockerfile\n    \u251c\u2500\u2500 LICENCE.md\n    \u251c\u2500\u2500 README.md\n    \u251c\u2500\u2500 assets\n    \u251c\u2500\u2500 bin\n    \u251c\u2500\u2500 conf\n    \u251c\u2500\u2500 docs\n    \u251c\u2500\u2500 environment.yml\n    \u251c\u2500\u2500 main.nf\n    \u251c\u2500\u2500 nextflow.config\n    \u2514\u2500\u2500 tests\n\n7 directories, 8 files\n```\n\n## Pipeline software licences\nSometimes 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.\n\n```console\n$ nf-core licences rnaseq\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nINFO: Warning: This tool only prints licence information for the software tools packaged using conda.\n        The pipeline may use other software and dependencies not described here.\n\nPackage Name           Version    Licence\n---------------------  ---------  --------------------\nstringtie              1.3.3      Artistic License 2.0\npreseq                 2.0.3      GPL\ntrim-galore            0.4.5      GPL\nbioconductor-edger     3.20.7     GPL >=2\nfastqc                 0.11.7     GPL >=3\nopenjdk                8.0.144    GPLv2\nr-gplots               3.0.1      GPLv2\nr-markdown             0.8        GPLv2\nrseqc                  2.6.4      GPLv2\nbioconductor-dupradar  1.8.0      GPLv3\nhisat2                 2.1.0      GPLv3\nmultiqc                1.5        GPLv3\nr-data.table           1.10.4     GPLv3\nstar                   2.5.4a     GPLv3\nsubread                1.6.1      GPLv3\npicard                 2.18.2     MIT\nsamtools               1.8        MIT\n```\n\n## Creating a new workflow\nThe `create` subcommand makes a new workflow using the nf-core base template.\nWith a given pipeline name, description and author, it makes a starter pipeline which follows nf-core best practices.\n\nAfter 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.\nSee the [nf-core syncing docs](https://nf-co.re/developers/sync) for more information.\n\n```console\n$ nf-core create\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\nWorkflow Name: nextbigthing\nDescription: This pipeline analyses data from the next big 'omics technique\nAuthor: Big Steve\n\nINFO: Creating new nf-core pipeline: nf-core/nextbigthing\n\nINFO: Initialising pipeline git repository\n\nINFO: Done. Remember to add a remote and push to GitHub:\n  cd /path/to/nf-core-nextbigthing\n  git remote add origin git@github.com:USERNAME/REPO_NAME.git\n  git push\n```\n\nOnce you have run the command, create a new empty repository on GitHub under your username (not the `nf-core` organisation, yet).\nOn your computer, add this repository as a git remote and push to it:\n\n```console\ngit remote add origin https://github.com/ewels/nf-core-nextbigthing.git\ngit push --set-upstream origin master\n```\n\nYou can then continue to edit, commit and push normally as you build your pipeline.\n\nPlease see the [nf-core documentation](https://nf-co.re/developers/adding_pipelines) for a full walkthrough of how to create a new nf-core workflow.\n\nNote 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.\n\n\n## Linting a workflow\nThe `lint` subcommand checks a given pipeline for all nf-core community guidelines.\nThis is the same test that is used on the automated continuous integration tests.\n\nFor example, the current version looks something like this:\n\n```console\n$ cd path/to/my_pipeline\n$ nf-core lint .\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\nRunning pipeline tests  [####################################]  100%  None\n\nINFO: ===========\n LINTING RESULTS\n=================\n  72 tests passed   2 tests had warnings   0 tests failed\n\nWARNING: Test Warnings:\n  http://nf-co.re/errors#8: Conda package is not latest available: picard=2.18.2, 2.18.6 available\n  http://nf-co.re/errors#8: Conda package is not latest available: bwameth=0.2.0, 0.2.1 available\n```\n\nYou can find extensive documentation about each of the lint tests in the [lint errors documentation](https://nf-co.re/errors).\n\n\n## Bumping a pipeline version number\n\nWhen 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!).\n\nThe command uses results from the linting process, so will only work with workflows that pass these tests.\n\nUsage is `nf-core bump-version <pipeline_dir> <new_version>`, eg:\n\n```console\n$ cd path/to/my_pipeline\n$ nf-core bump-version . 1.0\n\n                                          ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,'\n\n\nINFO: Running nf-core lint tests\nRunning pipeline tests  [####################################]  100%  None\n\nINFO: ===========\n LINTING RESULTS\n=================\n  96 tests passed   0 tests had warnings   0 tests failed\n\nINFO: Changing version number:\n  Current version number is '1.0dev'\n  New version number will be '1.0'\n\nINFO: Updating version in nextflow.config\n - version = '1.0dev'\n + version = '1.0'\n\nINFO: Updating version in nextflow.config\n - container = 'nfcore/mypipeline:dev'\n + container = 'nfcore/mypipeline:1.0'\n\nINFO: Updating version in .travis.yml\n - docker tag nfcore/mypipeline:dev nfcore/mypipeline:latest\n + docker tag nfcore/mypipeline:dev nfcore/mypipeline:1.0\n\nINFO: Updating version in Singularity\n - VERSION 1.0dev\n + VERSION 1.0\n\nINFO: Updating version in environment.yml\n - name: nf-core-mypipeline-1.0dev\n + name: nf-core-mypipeline-1.0\n\nINFO: Updating version in Dockerfile\n - PATH /opt/conda/envs/nf-core-mypipeline-1.0dev/bin:$PATH\n + PATH /opt/conda/envs/nf-core-mypipeline-1.0/bin:\\$PATH\n\nINFO: Updating version in Singularity\n - PATH=/opt/conda/envs/nf-core-mypipeline-1.0dev/bin:$PATH\n + PATH=/opt/conda/envs/nf-core-mypipeline-1.0/bin:\\$PATH\n```\n\nTo change the required version of Nextflow instead of the pipeline version number, use the flag `--nextflow`.\n\n## Citation\n\nIf you use `nf-core tools` in your work, please cite the `nf-core` preprint as follows:  \nEwels 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. 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