nf-core · apeltzer · Jun 12, 2018 · Jun 12, 2018
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,3 @@
 
 ## 2.0 - 2018-06-05
-Initial release of EAGER2.0, created with the NGI-NFcookiecutter template: https://github.com/nf-core/cookiecutter
+Initial release of nf-core/EAGER2, created with the NGI-NFcookiecutter template: https://github.com/nf-core/cookiecutter
diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,8 @@
 FROM nfcore/base
 MAINTAINER Alexander Peltzer <[email protected]>
 LABEL authors="[email protected]" \
-    description="Docker image containing all requirements for nf-EAGER pipeline"
+    description="Docker image containing all requirements for nf-core/EAGER2 pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-eager/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager2/bin:$PATH
diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 # ![nf-core/EAGER2](docs/images/EAGER2_logo.png)
 
-[![Build Status](https://travis-ci.org/apeltzer/nf-EAGER.svg?branch=master)](https://travis-ci.org/apeltzer/nf-EAGER)
+[![Build Status](https://travis-ci.org/nf-core/EAGER2.svg?branch=master)](https://travis-ci.org/nf-core/EAGER2)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.27.0-brightgreen.svg)](https://www.nextflow.io/)
 [![Gitter](https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg)](https://gitter.im/nf-core/EAGER2)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
-[![Docker Container available](https://img.shields.io/docker/automated/nfcore/rnaseq.svg)](https://hub.docker.com/r/nfcore/eager2/)
+[![Docker Container available](https://img.shields.io/docker/automated/nfcore/eager2.svg)](https://hub.docker.com/r/nfcore/eager2/)
 ![Singularity Container available](
 https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
@@ -34,7 +34,7 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
 
 
 ### Documentation
-The nf-EAGER pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+The nf-core/EAGER2 pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
 1. [Installation](docs/installation.md)
 2. Pipeline configuration

diff --git a/assets/email_template.html b/assets/email_template.html
@@ -5,19 +5,19 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-EAGER: A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.">
-  <title>nf-EAGER Pipeline Report</title>
+  <meta name="description" content="nf-core/EAGER2: A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.">
+  <title>nf-core/EAGER2 Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<h1>nf-EAGER v${version}</h1>
+<h1>nf-core/EAGER2 v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-EAGER execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">nf-core/EAGER2 execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>

diff --git a/assets/email_template.txt b/assets/email_template.txt
@@ -1,13 +1,13 @@
 ========================================
- nf-EAGER v${version}
+ nf-core/EAGER2 v${version}
 ========================================
 Run Name: $runName
 
 <% if (success){
-    out << "## nf-EAGER execution completed successfully! ##"
+    out << "## nf-core/EAGER2 execution completed successfully! ##"
 } else {
     out << """####################################################
-## nf-EAGER execution completed unsuccessfully! ##
+## nf-core/EAGER2 execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -19,15 +19,15 @@ ${errorReport}
 
 <% if (!success){
     out << """####################################################
-## nf-EAGER execution completed unsuccessfully! ##
+## nf-core/EAGER2 execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
 
 ${errorReport}
 """
 } else {
-    out << "## nf-EAGER execution completed successfully! ##"
+    out << "## nf-core/EAGER2 execution completed successfully! ##"
 }
 %>
 
@@ -52,5 +52,5 @@ Software Versions:
 <% out << software_versions.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf-EAGER
-https://github.com/apeltzer/nf-EAGER
+nf-core/EAGER2
+https://github.com/nf-core/EAGER2
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
@@ -4,13 +4,13 @@
 import re
 
 regexes = {
-    'nf-EAGER': ['v_pipeline.txt', r"(\S+)"],
+    'nf-core/EAGER2': ['v_pipeline.txt', r"(\S+)"],
     'Nextflow': ['v_nextflow.txt', r"(\S+)"],
     'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
     'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
 }
 results = OrderedDict()
-results['nf-EAGER'] = '<span style="color:#999999;\">N/A</span>'
+results['nf-core/EAGER2'] = '<span style="color:#999999;\">N/A</span>'
 results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
 results['FastQC'] = '<span style="color:#999999;\">N/A</span>'
 results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
@@ -26,8 +26,8 @@
 # Dump to YAML
 print ('''
 id: 'nf-eager-software-versions'
-section_name: 'nf-EAGER Software Versions'
-section_href: 'https://github.com/apeltzer/nf-EAGER'
+section_name: 'nf-core/EAGER2 Software Versions'
+section_href: 'https://github.com/nf-core/EAGER2'
 plot_type: 'html'
 description: 'are collected at run time from the software output.'
 data: |

diff --git a/conf/base.config b/conf/base.config
@@ -1,6 +1,6 @@
 /*
  * -------------------------------------------------
- *  nf-EAGER Nextflow base config file
+ *  nf-core/EAGER2 Nextflow base config file
  * -------------------------------------------------
  * A 'blank slate' config file, appropriate for general
  * use on most high performace compute environments.

diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
@@ -1,7 +1,7 @@
 report_comment: >
-    This report has been generated by the <a href="https://github.com/apeltzer/nf-EAGER" target="_blank">nf-EAGER</a>
+    This report has been generated by the <a href="https://github.com/nf-core/EAGER2" target="_blank">nf-core/EAGER2</a>
     analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://github.com/apeltzer/nf-EAGER" target="_blank">documentation</a>.
+    <a href="https://github.com/nf-core/EAGER2" target="_blank">documentation</a>.
 report_section_order:
     nf-eager-software-versions:
         order: -1000
diff --git a/docs/README.md b/docs/README.md
@@ -1,6 +1,6 @@
-# nf-EAGER Documentation
+# nf-core/EAGER2 Documentation
 
-The nf-EAGER documentation is split into the following files:
+The nf-core/EAGER2 documentation is split into the following files:
 
 1. [Installation](installation.md)
 2. Pipeline configuration

diff --git a/docs/configuration/adding_your_own.md b/docs/configuration/adding_your_own.md
@@ -1,4 +1,4 @@
-# nf-EAGER: Configuration for other clusters
+# nf-core/EAGER2: Configuration for other clusters
 
 It is entirely possible to run this pipeline on other clusters, though you will need to set up your own config file so that the pipeline knows how to work with your cluster.
 
@@ -35,18 +35,18 @@ process {
 To run the pipeline, several software packages are required. How you satisfy these requirements is essentially up to you and depends on your system. If possible, we _highly_ recommend using either Docker or Singularity.
 
 ### Docker
-Docker is a great way to run nf-EAGER, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
+Docker is a great way to run nf-core/EAGER2, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
 
 Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required.
 
 First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
 
 Then, simply run the analysis pipeline:
 ```bash
-nextflow run apeltzer/nf-EAGER -profile docker --reads '<path to your reads>'
+nextflow run nf-core/EAGER2 -profile docker --reads '<path to your reads>'
 ```
 
-Nextflow will recognise `apeltzer/nf-EAGER` and download the pipeline from GitHub. The `-profile docker` configuration lists the [quay.io/nf-core/nf-eager](https://hub.docker.com/r/quay.io/nf-core/nf-eager/) image that we have created and is hosted at dockerhub, and this is downloaded.
+Nextflow will recognise `nf-core/EAGER2` and download the pipeline from GitHub. The `-profile docker` configuration lists the [nfcore/eager2](https://hub.docker.com/r/nfcore/eager2/) image that we have created and is hosted at dockerhub, and this is downloaded.
 
 The public docker images are tagged with the same version numbers as the code, which you can use to ensure reproducibility. When running the pipeline, specify the pipeline version with `-r`, for example `-r v1.3`. This uses pipeline code and docker image from this tagged version.
 
@@ -63,12 +63,12 @@ process {
 
 The variable `wf_container` is defined dynamically and automatically specifies the image tag if Nextflow is running with `-r`.
 
-A test suite for docker comes with the pipeline, and can be run by moving to the [`tests` directory](https://github.com/apeltzer/nf-EAGER/tree/master/tests) and running `./run_test.sh`. This will download a small yeast genome and some data, and attempt to run the pipeline through docker on that small dataset. This is automatically run using [Travis](https://travis-ci.org/apeltzer/nf-EAGER/) whenever changes are made to the pipeline.
+A test suite for docker comes with the pipeline, and can be run by moving to the [`tests` directory](https://github.com/nf-core/EAGER2/tree/master/tests) and running `./run_test.sh`. This will download a small yeast genome and some data, and attempt to run the pipeline through docker on that small dataset. This is automatically run using [Travis](https://travis-ci.org/nf-core/EAGER2/) whenever changes are made to the pipeline.
 
 ### Singularity image
 Many HPC environments are not able to run Docker due to security issues. [Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker. Even better, it can use create images directly from dockerhub.
 
-To use the singularity image for a single run, use `-with-singularity 'docker://apeltzer/nf-EAGER'`. This will download the docker container from dockerhub and create a singularity image for you dynamically.
+To use the singularity image for a single run, use `-with-singularity 'docker://nfcore/eager2'`. This will download the docker container from dockerhub and create a singularity image for you dynamically.
 
 To specify singularity usage in your pipeline config file, add the following:
 
@@ -88,13 +88,13 @@ If you intend to run the pipeline offline, nextflow will not be able to automati
 First, pull the image file where you have an internet connection:
 
 ```bash
-singularity pull --name nf-eager.img docker://apeltzer/nf-EAGER
+singularity pull --name eager2.img docker://nfcore/eager2
 ```
 
 Then transfer this file and run the pipeline with this path:
 
 ```bash
-nextflow run /path/to/nf-eager -with-singularity /path/to/nf-eager.img
+nextflow run /path/to/eager2 -with-singularity /path/to/eager2.img
 ```
 
 
@@ -120,8 +120,8 @@ conda config --add channels salilab
 
 #### 3) Create a conda environment, with all necessary packages:
 ```bash
-conda create --name nf-eager_py2.7 python=2.7
-source activate nf-eager_py2.7
+conda create --name nf-core-eager2_py2.7 python=2.7
+source activate nf-core-eager2_py2.7
 conda install --yes \
     fastqc \
     multiqc
@@ -132,7 +132,7 @@ _(Feel free to adjust versions as required.)_
 Once created, the conda environment can be activated before running the pipeline and deactivated afterwards:
 
 ```bash
-source activate nf-eager_py2.7
+source activate nf-core-eager2_py2.7
 # run pipeline
 source deactivate
 ```
diff --git a/docs/configuration/local.md b/docs/configuration/local.md
@@ -1,20 +1,20 @@
-# nf-EAGER: Local Configuration
+# nf-core/EAGER2: Local Configuration
 
 If running the pipeline in a local environment, we highly recommend using either Docker or Singularity.
 
 ## Docker
-Docker is a great way to run nf-EAGER, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
+Docker is a great way to run nf-core/EAGER2, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.
 
-Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required. The nf-EAGER profile comes with a configuration profile for docker, making it very easy to use. This also comes with the required presets to use the AWS iGenomes resource, meaning that if using common reference genomes you just specify the reference ID and it will be autaomtically downloaded from AWS S3.
+Nextflow has [excellent integration](https://www.nextflow.io/docs/latest/docker.html) with Docker, and beyond installing the two tools, not much else is required. The nf-core/EAGER2 profile comes with a configuration profile for docker, making it very easy to use. This also comes with the required presets to use the AWS iGenomes resource, meaning that if using common reference genomes you just specify the reference ID and it will be automatically downloaded from AWS S3.
 
 First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
 
 Then, simply run the analysis pipeline:
 ```bash
-nextflow run apeltzer/nf-EAGER -profile docker --reads '<path to your reads>'
+nextflow run nf-core/EAGER2 -profile docker --reads '<path to your reads>'
 ```
 
-Nextflow will recognise `apeltzer/nf-EAGER` and download the pipeline from GitHub. The `-profile docker` configuration lists the [quay.io/nf-core/nf-eager](https://hub.docker.com/r/quay.io/nf-core/nf-eager/) image that we have created and is hosted at dockerhub, and this is downloaded.
+Nextflow will recognise `nf-core/EAGER2` and download the pipeline from GitHub. The `-profile docker` configuration lists the [nf-core/eager2](https://hub.docker.com/r/nfcore/eager2/) image that we have created and is hosted at dockerhub, and this is downloaded.
 
 For more information about how to work with reference genomes, see [`docs/configuration/reference_genomes.md`](docs/configuration/reference_genomes.md).
 
@@ -25,18 +25,18 @@ The public docker images are tagged with the same version numbers as the code, w
 ## Singularity image
 Many HPC environments are not able to run Docker due to security issues. [Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker. Even better, it can use create images directly from dockerhub.
 
-To use the singularity image for a single run, use `-with-singularity 'docker://quay.io/nf-core/nf-eager'`. This will download the docker container from dockerhub and create a singularity image for you dynamically.
+To use the singularity image for a single run, use `-with-singularity 'docker://nfcore/eager2'`. This will download the docker container from dockerhub and create a singularity image for you dynamically.
 
 If you intend to run the pipeline offline, nextflow will not be able to automatically download the singularity image for you. Instead, you'll have to do this yourself manually first, transfer the image file and then point to that.
 
 First, pull the image file where you have an internet connection:
 
 ```bash
-singularity pull --name nf-eager.img docker://quay.io/nf-core/nf-eager
+singularity pull --name nf-core-eager2.img docker://nfcore/eager2
 ```
 
 Then transfer this file and run the pipeline with this path:
 
 ```bash
-nextflow run /path/to/nf-EAGER -with-singularity /path/to/nf-eager.img
+nextflow run /path/to/nf-core/EAGER2 -with-singularity /path/to/nf-core-eager2.img
 ```
diff --git a/docs/configuration/reference_genomes.md b/docs/configuration/reference_genomes.md
@@ -1,11 +1,11 @@
-# nf-EAGER: Reference Genomes Configuration
+# nf-core/EAGER2: Reference Genomes Configuration
 
-The nf-EAGER pipeline needs a reference genome for alignment and annotation. If not already available, start by downloading the relevant reference, for example from [illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
+The nf-core/EAGER2 pipeline needs a reference genome for alignment and annotation. If not already available, start by downloading the relevant reference, for example from [illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
 
 The minimal requirements are a FASTA file.
 
 ## Adding paths to a config file
-Specifying long paths every time you run the pipeline is a pain. To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline. 
+Specifying long paths every time you run the pipeline is a pain. To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline.
 
 Note that this genome key can also be specified in a config file if you always use the same genome.
 
@@ -36,7 +36,7 @@ If possible, we recommend making this resource available on your cluster. We hav
 To add iGenomes to your config file, add the following line to the end of your config file:
 
 ```nextflow
-includeConfig '/path/to/nf-EAGER/conf/igenomes.config'
+includeConfig '/path/to/nf-core/EAGER2/conf/igenomes.config'
 ```
 
 This works best when you have a `profile` set up in the pipeline - see [`nextflow.config`](../../nextflow.config).

diff --git a/docs/installation.md b/docs/installation.md
@@ -1,6 +1,6 @@
-# nf-EAGER Installation
+# nf-core/EAGER2 Installation
 
-To start using the nf-EAGER pipeline, there are three steps described below:
+To start using the nf-core/EAGER2 pipeline, there are three steps described below:
 
 1. [Install Nextflow](#install-nextflow)
 2. [Install the pipeline](#install-the-pipeline)
@@ -26,10 +26,11 @@ mv nextflow ~/bin
 
 **You need NextFlow version >= 0.24 to run this pipeline.**
 
-See [nextflow.io](https://www.nextflow.io/) and [NGI-NextflowDocs](https://github.com/SciLifeLab/NGI-NextflowDocs) for further instructions on how to install and configure Nextflow.
+See [Nextflow documentation](https://www.nextflow.io/docs/latest/index.html) or the [nf-core website](https://nf-core.github.io/) for further instructions on how to install and configure Nextflow.
+Join the gitter channels for some direct contact with developers: [nextflow channel](https://gitter.im/nextflow-io/nextflow) or [nf-core Lobby](https://gitter.im/nf-core/Lobby).
 
 ## 2) Install the Pipeline
-This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `apeltzer/nf-EAGER` is specified as the pipeline name.
+This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if `nf-core/EAGER2` is specified as the pipeline name.
 
 ### Offline use
 

diff --git a/docs/output.md b/docs/output.md
@@ -1,4 +1,4 @@
-# nf-EAGER
+# nf-core/EAGER2
 A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.
 
 This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

diff --git a/docs/parameters.md b/docs/parameters.md
@@ -1,4 +1,4 @@
-# Adjustable parameters for EAGER2
+# Adjustable parameters for nf-core/EAGER2
 
 ## Read Clipping / Merging
 params.mergemethod = AdapterRemoval or ClipAndMerge (choice)