Merge pull request #27 from nf-core/development

Prepare release 1.1.0

.travis.yml

@@ -1,16 +1,19 @@
 sudo: required
-language: java
+language: python
 jdk: openjdk8
 services:
   - docker
 python:
-  - "2.7"
+  - '3.6'
 cache: pip
 matrix:
   fast_finish: true
 
 before_install:
-  - docker pull nfcore/hlatyping:1.0.0
+  # PRs made to 'master' branch should always orginate from another repo or the 'dev' branch
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "development" ])'
+  - docker pull nfcore/hlatyping
+  - docker tag nfcore/hlatyping nfcore/hlatyping:1.1.0
 
 install:
   # Install Nextflow
@@ -19,14 +22,12 @@ install:
   - wget -qO- get.nextflow.io | bash
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
   # Install nf-core/tools
-  - git clone https://github.com/nf-core/tools.git /tmp/nf-core-tools
-  - cd /tmp/nf-core-tools
-  - pip install --user -e .
+  - pip install nf-core
   # Reset
   - cd ${TRAVIS_BUILD_DIR}
 
 env:
-  - NXF_VER=0.30.2 # Specify a minimum NF version that should be tested and work
+  - NXF_VER=0.31.0 # Specify a minimum NF version that should be tested and work
   - NXF_VER='' # Plus: get the latest NF version and check, that it works
 
 script:

CHANGELOG.md

@@ -1,5 +1,6 @@
-## 1.1.0 - aqua-titanium-crab - 2018-08-03
+## 1.1.0 - aqua-titanium-crab - 2018-08-14
 
+- Fix [#17](https://github.com/nf-core/hlatyping/issues/17)
 - Fix [#13](https://github.com/nf-core/hlatyping/issues/13)
 - Fix [#12](https://github.com/nf-core/hlatyping/issues/12)
 - New profile `full_trace` that can be used for full trace info broadcast with Nextflow's `weblog feature`

Dockerfile

@@ -4,5 +4,5 @@ LABEL authors="[email protected]" \
     description="Docker image containing all requirements for nf-core/hlatyping pipeline"
 
 COPY environment.yml /
-RUN conda env update -n root -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nfcore-hlatyping-1.0.0/bin:$PATH
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-hlatyping-1.1.0/bin:$PATH

README.md

@@ -2,7 +2,7 @@
 Precision HLA typing from next-generation sequencing data using [OptiType](https://github.com/FRED-2/OptiType).
 
 [![Build Status](https://travis-ci.org/nf-core/hlatyping.svg?branch=master)](https://travis-ci.org/nf-core/hlatyping)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.30.2-brightgreen.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.31.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/hlatyping.svg)](https://hub.docker.com/r/nfcore/hlatyping)

Singularity

@@ -10,5 +10,9 @@ Bootstrap:docker
     environment.yml /
 
 %post
-    /opt/conda/bin/conda env update -n root -f /environment.yml
+    /opt/conda/bin/conda env create -f /environment.yml
     /opt/conda/bin/conda clean -a
+    PATH=/opt/conda/envs/nf-core-hlatyping-1.1.0/bin:$PATH
+    export PATH
+
+

conf/singularity.config

@@ -11,4 +11,4 @@ singularity {
   enabled = true
 }
 
-params.container = 'shub://nf-core/hlatyping:1.0.0'
+params.container = 'shub://nf-core/hlatyping:1.1.0'

environment.yml

@@ -1,4 +1,4 @@
-name: nfcore-hlatyping-1.1.0
+name: nf-core-hlatyping-1.1.0
 channels:
   - bioconda
   - conda-forge

nextflow.config

@@ -86,9 +86,12 @@ dag {
 }
 
 manifest {
-  homePage = 'https://github.com/nf-core/hlatyping'
+  name = 'nf-core/hlatyping'
+  pipelineVersion = '1.1.0'
+  nextflowVersion = '>=0.31.0'
   description = 'Precision HLA typing from next-generation sequencing data.'
   mainScript = 'main.nf'
+  homePage = 'https://github.com/nf-core/hlatyping'
 }
 
 // Function to ensure that resource requirements don't go beyond