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apeltzer merged 1 commit into from
Mar 31, 2019
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Improve Readme ToC #293

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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -10,7 +10,7 @@
* Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available
* Fix bugs in `nf-core download`
* The _latest_ release is now fetched by default if not specified
* Downloaded pipeline files are now properly executable
* Downloaded pipeline files are now properly executable.

## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark

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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -3,5 +3,5 @@ LABEL authors="[email protected],[email protected]"
description="Docker image containing base requirements for the nfcore pipelines"

# Install procps so that Nextflow can poll CPU usage
RUN apt-get update && apt-get install -y procps && apt-get clean -y
RUN apt-get update && apt-get install -y procps && apt-get clean -y
RUN conda install conda=4.6.7
24 changes: 17 additions & 7 deletions README.md
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Expand Up @@ -9,13 +9,17 @@ A python package with helper tools for the nf-core community.

## Table of contents

* [Installation](#installation)
* [Listing pipelines](#listing-pipelines) (`nf-core list`)
* [Downloading pipelines for offline use](#downloading-pipelines-for-offline-use) (`nf-core download`)
* [Listing software licences](#pipeline-software-licences): List software licences for a given workflow (`nf-core licences`)
* [Creating a new workflow](#creating-a-new-workflow) (`nf-core create`)
* [Checking a pipeline against nf-core guidelines](#linting-a-workflow) (`nf-core lint`)
* [Bumping a pipeline version number](#bumping-a-pipeline-version-number) (`nf-core bump-version`)
* [`nf-core` tools installation](#installation)
* [`nf-core list` - List available pipelines](#listing-pipelines)
* [`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` - Change a 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

Expand All @@ -25,6 +29,12 @@ You can install `nf-core/tools` from [PyPI](https://pypi.python.org/pypi/nf-core
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
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