Merge pull request #112 from nf-core/dev

PR for release 1.1.1

.github/markdownlint.yml

@@ -1,9 +1,5 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
-    siblings_only: true
+    siblings_only: true

.github/workflows/branch.yml

@@ -0,0 +1,16 @@
+name: ampliseq branch protection
+# This workflow is triggered on PRs to master branch on the repository
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      # PRs are only ok if coming from an nf-core dev branch
+      - uses: actions/checkout@v1
+      - name: Check PRs
+        run: |
+          { [[ $(git remote get-url origin) == *nf-core/ampliseq ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == patch* ]]

.github/workflows/ci.yml

@@ -0,0 +1,26 @@
+name: nf-core CI
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on: [push, pull_request]  
+
+jobs:
+  test:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['19.10.0', '']
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          export NXF_VER=${{ matrix.nxf_ver }}
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Run test
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+      - name: Run multi test
+        run: | 
+          nextflow run ${GITHUB_WORKSPACE} -profile test_multi,docker
+

.github/workflows/linting.yml

@@ -0,0 +1,41 @@
+name: nf-core linting
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+on: [push, pull_request]  
+
+jobs:
+  Markdown:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-node@v1
+        with:
+          node-version: '10'
+      - name: Install markdownlint
+        run: |
+          npm install -g markdownlint-cli
+      - name: Run Markdownlint
+        run: |
+          markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+  nf-core:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - uses: actions/setup-python@v1
+        with:
+          python-version: '3.6'
+          architecture: 'x64'
+      - name: Install pip
+        run: |
+          sudo apt install python3-pip
+          pip install --upgrade pip
+      - name: Install nf-core tools
+        run: |
+          pip install nf-core
+      - name: Run nf-core lint
+        run: |
+          nf-core lint ${GITHUB_WORKSPACE}

.travis.yml

@@ -9,11 +9,10 @@ matrix:
 
 before_install:
   # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
-  # Pull the docker image first so the test doesn't wait for this
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'  # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/ampliseq:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/ampliseq:dev nfcore/ampliseq:1.1.0
+  - docker tag nfcore/ampliseq:dev nfcore/ampliseq:dev
 
 install:
   # Install Nextflow
@@ -30,7 +29,7 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER=18.10.1 # Specify a minimum NF version that should be tested and work
+  - NXF_VER='19.10.0' # 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

@@ -1,8 +1,19 @@
 # nf-core/ampliseq
 
+## nf-core/ampliseq version 1.1.1 - 2019
+
+### Pipeline Updates
+
+* Update from QIIME2 v2018.6 to v2019.10, including DADA2 v1.6 to DADA2 v1.10
+
+### Bugfixes
+
+* [#78](https://github.com/nf-core/ampliseq/issues/78) - All sequenced classifed to the same species
+
 ## nf-core/ampliseq version 1.1.0 "Silver Lime Bee" - 2019
 
-#### Pipeline updates
+### Pipeline updates
+
 * [#40](https://github.com/nf-core/ampliseq/issues/40) - Added support for data originating from multiple sequencing runs
 * [#53](https://github.com/nf-core/ampliseq/issues/53) - DADA2 report is always exported
 * [#49](https://github.com/nf-core/ampliseq/issues/49) - Allowed more filtering options
@@ -13,9 +24,11 @@
 * [#63](https://github.com/nf-core/ampliseq/issues/63) - QIIME imports files by using a manifest, giving more freedom with input file names
 * [#84](https://github.com/nf-core/ampliseq/issues/84) - Add proper nf-core logo
 
-#### Bug fixes
+### Bug fixes
+
 * [#57](https://github.com/nf-core/ampliseq/issues/57) - Indicate exact regex for sequencing file names
 * [#60](https://github.com/nf-core/ampliseq/issues/60) - publish demux.qza when --untilQ2import
 
 ## nf-core/ampliseq version 1.0.0 "Olive Steel Panda" - 2018-11-23
+
 Initial release of nf-core/ampliseq, created with the [nf-core](http://nf-co.re/) template.

Dockerfile

@@ -1,11 +1,10 @@
-FROM nfcore/base
+FROM nfcore/base:1.7
 LABEL description="Docker image containing all requirements for nf-core/ampliseq pipeline"
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-ampliseq-1.1.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-ampliseq-dev/bin:$PATH
 ## Required to build the container properly
 RUN mkdir -p /root/.config/matplotlib
 RUN echo "backend : Agg" > /root/.config/matplotlib/matplotlibrc
 ## Don't recache on each execution, do that once per build process
 RUN qiime dev refresh-cache
-

README.md

@@ -1,17 +1,17 @@
 # ![nf-core/ampliseq](docs/images/nfcore-ampliseq_logo.png)
 
-[![Build Status](https://travis-ci.com/nf-core/ampliseq.svg?branch=master)](https://travis-ci.com/nf-core/ampliseq)[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A518.10.1-brightgreen.svg)](https://www.nextflow.io/)
+[![Build Status](https://github.com/nf-core/ampliseq/workflows/ampliseq%20CI/badge.svg)](https://github.com/nf-core/ampliseq/workflows/ampliseq%20CI/badge.svg)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-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/ampliseq.svg)](https://hub.docker.com/r/nfcore/ampliseq)
-![Singularity Container available](
-https://img.shields.io/badge/singularity-available-7E4C74.svg)
+[![DOI](https://zenodo.org/badge/150448201.svg)](https://zenodo.org/badge/latestdoi/150448201)
 
-### Introduction
+## Introduction
 
 **nfcore/ampliseq** is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.
 
-The workflow processes raw data from FastQ inputs ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)), trims primer sequences from the reads ([Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)), imports data into [QIIME2](https://qiime2.org/), generates amplicon sequencing variants (ASV, [DADA2](https://www.nature.com/articles/nmeth.3869)), classifies features against the [SILVA](https://www.arb-silva.de/) [v132](https://www.arb-silva.de/documentation/release-132/) database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof, and finally calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277)). See the [output documentation](docs/output.md) for more details of the results.
+The workflow processes raw data from FastQ inputs ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)), trims primer sequences from the reads ([Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)), imports data into [QIIME2](https://www.nature.com/articles/s41587-019-0209-9), generates amplicon sequencing variants (ASV, [DADA2](https://www.nature.com/articles/nmeth.3869)), classifies features against the [SILVA](https://www.arb-silva.de/) [v132](https://www.arb-silva.de/documentation/release-132/) database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof, and finally calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277)). See the [output documentation](docs/output.md) for more details of the results.
 
 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.
 

conf/base.config

@@ -64,6 +64,9 @@ process {
     memory = { check_max (16.GB * task.attempt, 'memory' ) }
     time = { check_max (2.h * task.attempt, 'time' ) }
   }
+  withName: alpha_diversity {
+    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
+  }
 }
 
 params {

conf/test.config

@@ -17,7 +17,7 @@ params {
   // Input data
   FW_primer = "GTGYCAGCMGCCGCGGTAA"
   RV_primer = "GGACTACNVGGGTWTCTAAT"
-  classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza"
+  classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-gg_13_8-85-qiime2_2019.7-classifier.qza"
   metadata = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/Metadata.tsv"
   outdir = "./results"
   temp_dir = "./results/tmp_dir"

conf/test_multi.config

@@ -17,7 +17,7 @@ params {
   // Input data
   FW_primer = "GTGYCAGCMGCCGCGGTAA"
   RV_primer = "GGACTACNVGGGTWTCTAAT"
-  classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza"
+  classifier = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-gg_13_8-85-qiime2_2019.7-classifier.qza"
   metadata = "https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/Metadata_multi.tsv"
   outdir = "./results"
   temp_dir = "./results/tmp_dir"