Merge pull request #28 from drpatelh/master

Bump version for 1.0.0 release

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/atacseq:dev
   # Fake the tag locally so that the pipeline runs properly
   # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/atacseq:dev nfcore/atacseq:dev
+  - docker tag nfcore/atacseq:dev nfcore/atacseq:1.0.0
 
 install:
   # Install Nextflow

Dockerfile

@@ -4,4 +4,4 @@ LABEL authors="harshil.patel@crick.ac.uk" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-atacseq-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-atacseq-1.0.0/bin:$PATH

README.md

@@ -11,7 +11,7 @@
 
 **nfcore/atacseq** is a bioinformatics analysis pipeline used for ATAC-seq data.
 
-The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
 
 ### Pipeline summary
 
@@ -56,14 +56,14 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 ### Documentation
 The nf-core/atacseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation](docs/installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
-    * [Local installation](docs/configuration/local.md)
-    * [Adding your own system](docs/configuration/adding_your_own.md)
-    * [Reference genomes](docs/configuration/reference_genomes.md)
+    * [Local installation](https://nf-co.re/usage/local_installation)
+    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
 3. [Running the pipeline](docs/usage.md)
 4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](docs/troubleshooting.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
 ### Credits
 

docs/README.md

@@ -2,11 +2,11 @@
 
 The nf-core/atacseq documentation is split into the following files:
 
-1. [Installation](installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
-    * [Local installation](configuration/local.md)
-    * [Adding your own system](configuration/adding_your_own.md)
-    * [Reference genomes](configuration/reference_genomes.md)
+    * [Local installation](https://nf-co.re/usage/local_installation)
+    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
 3. [Running the pipeline](usage.md)
 4. [Output and how to interpret the results](output.md)
-5. [Troubleshooting](troubleshooting.md)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)