Merge pull request #130 from nf-core/dev

Release 1.1.1

.github/CONTRIBUTING.md

@@ -54,4 +54,4 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/mag documentation](https://nf-co.re/mag/docs) and don't hesitate to get in touch on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/mag documentation](https://nf-co.re/mag/usage) and don't hesitate to get in touch on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -36,7 +36,7 @@ Steps to reproduce the behaviour:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/mag:1.0.0] -->
 

.github/markdownlint.yml

@@ -3,3 +3,7 @@ default: true,
 line-length: false
 no-duplicate-header:
     siblings_only: true
+no-inline-html:
+    allowed_elements:
+        - img
+        - p

.github/workflows/awsfulltest.yml

@@ -1,10 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 jobs:
   run-awstest:
@@ -20,10 +22,6 @@ jobs:
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
-        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -37,4 +35,4 @@ jobs:
             --job-name nf-core-mag \
             --job-queue $AWS_JOB_QUEUE \
             --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["nf-core/mag", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/mag/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/mag/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+            --container-overrides '{"command": ["nf-core/mag", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/mag/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/mag/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/awstest.yml

@@ -1,11 +1,10 @@
 name: nf-core AWS test
 # This workflow is triggered on push to the master branch.
-# It runs the -profile 'test' on AWS batch
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
 
 jobs:
   run-awstest:

.github/workflows/ci.yml

@@ -34,13 +34,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/mag:1.1.0
+        run: docker build --no-cache . -t nfcore/mag:1.1.1
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/mag:dev
-          docker tag nfcore/mag:dev nfcore/mag:1.1.0
+          docker tag nfcore/mag:dev nfcore/mag:1.1.1
 
       - name: Check if BUSCO Dockerfile or Conda environment changed
         uses: technote-space/get-diff-action@v1
@@ -51,13 +51,13 @@ jobs:
 
       - name: Build new docker image for BUSCO
         if: env.GIT_DIFF
-        run: docker build --no-cache ./containers/busco/ -t nfcore/magbusco:1.1.0
+        run: docker build --no-cache ./containers/busco/ -t nfcore/magbusco:1.1.1
 
       - name: Pull docker image for BUSCO
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/magbusco:dev
-          docker tag nfcore/magbusco:dev nfcore/magbusco:1.1.0
+          docker tag nfcore/magbusco:dev nfcore/magbusco:1.1.1
 
       - name: Install Nextflow
         run: |

CHANGELOG.md

@@ -3,6 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.1 - 2019/11/10
+
+### `Added`
+
+- [#121](https://github.com/nf-core/mag/pull/121) - Add full-size test
+- [#124](https://github.com/nf-core/mag/pull/124) - Add worfklow overview figure to `README`
+
+### `Changed`
+
+- [#123](https://github.com/nf-core/mag/pull/123) - Update to new nf-core 1.11 `TEMPLATE`
+
+### `Fixed`
+
+- [#118](https://github.com/nf-core/mag/pull/118) - Fix `seaborn` to `v0.10.1` to avoid `nanoplot` error
+- [#120](https://github.com/nf-core/mag/pull/120) - Fix link to CAT database in help message
+- [#124](https://github.com/nf-core/mag/pull/124) - Fix description of `CAT` process in `output.md`
+
 ## v1.1.0 - 2020/10/06
 
 ### `Added`

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.2
+FROM nfcore/base:1.11
 LABEL authors="Hadrien Gourlé <hadrien.gourle@slu.se>, Daniel Straub <d4straub@gmail.com>, Sabrina Krakau <sabrinakrakau@gmail.com>" \
       description="Docker image containing all software requirements for the nf-core/mag pipeline"
 
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-mag-1.1.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mag-1.1.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-mag-1.1.0 > nf-core-mag-1.1.0.yml
+RUN conda env export --name nf-core-mag-1.1.1 > nf-core-mag-1.1.1.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

README.md

@@ -14,43 +14,48 @@
 ## Introduction
 
 This pipeline is for assembly, binning, and annotation of metagenomes.
-It supports both short and long reads, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [porechop](https://github.com/rrwick/Porechop), and performs basic QC with [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
 
-The pipeline then:
-
-* assigns taxonomy to reads using [centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [kraken2](https://github.com/DerrickWood/kraken2/wiki)
-* performs assembly using [megahit](https://github.com/voutcn/megahit) and [spades](http://cab.spbu.ru/software/spades/), and checks their quality using [quast](http://quast.sourceforge.net/quast)
-* performs metagenome binning using [metabat2](https://bitbucket.org/berkeleylab/metabat/src/master/), and checks the quality of the genome bins using [busco](https://busco.ezlab.org/)
-
-Furthermore, the pipeline creates various reports in the results directory specified, including a [multiqc](https://multiqc.info/) report summarizing some of the findings and software versions.
+<p align="center">
+    <img src="docs/images/mag_workflow.png" alt="nf-core/mag workflow overview" width="60%">
+</p>
 
 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.
 
 ## Quick Start
 
 1. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-2. Install either [`Docker`](https://docs.docker.com/engine/installation/) or [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```bash
-    nextflow run nf-core/mag -profile test,<docker/singularity/conda/institute>
+    nextflow run nf-core/mag -profile test,<docker/singularity/podman/conda/institute>
     ```
 
     > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
 
 4. Start running your own analysis!
 
     ```bash
-    nextflow run nf-core/mag -profile <docker/singularity/conda/institute> --input '*_R{1,2}.fastq.gz'
+    nextflow run nf-core/mag -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz'
     ```
 
-See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+See [usage docs](https://nf-co.re/mag/usage) for all of the available options when running the pipeline.
 
 ## Documentation
 
-The nf-core/mag pipeline comes with documentation about the pipeline which you can read at [https://nf-co.re/mag](https://nf-co.re/mag) or find in the [`docs/` directory](docs).
+The nf-core/mag pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/mag/usage) and [output](https://nf-co.re/mag/output).
+
+In short, it supports both short and long reads, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [porechop](https://github.com/rrwick/Porechop), and performs basic QC with [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+The pipeline then:
+
+* assigns taxonomy to reads using [centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [kraken2](https://github.com/DerrickWood/kraken2/wiki)
+* performs assembly using [megahit](https://github.com/voutcn/megahit) and [spades](http://cab.spbu.ru/software/spades/), and checks their quality using [quast](http://quast.sourceforge.net/quast)
+* performs metagenome binning using [metabat2](https://bitbucket.org/berkeleylab/metabat/src/master/), and checks the quality of the genome bins using [busco](https://busco.ezlab.org/)
+* assigns taxonomy to bins using [CAT](https://github.com/dutilh/CAT)
+
+Furthermore, the pipeline creates various reports in the results directory specified, including a [multiqc](https://multiqc.info/) report summarizing some of the findings and software versions.
 
 ## Credits
 

conf/base.config

@@ -106,23 +106,23 @@ process {
     time = { check_max (8.h * task.attempt, 'time' ) }
   }
   withName: busco {
-    container = 'nfcore/magbusco:1.1.0'
+    container = 'nfcore/magbusco:1.1.1'
     profiles {
       conda {
         conda = "$baseDir/containers/busco/environment.yml"
       }
     }
   }
   withName: busco_plot {
-    container = 'nfcore/magbusco:1.1.0'
+    container = 'nfcore/magbusco:1.1.1'
     profiles {
       conda {
         conda = "$baseDir/containers/busco/environment.yml"
       }
     }
   }
   withName: get_busco_version {
-    container = 'nfcore/magbusco:1.1.0'
+    container = 'nfcore/magbusco:1.1.1'
     profiles {
       conda {
         conda = "$baseDir/containers/busco/environment.yml"

conf/test.config

@@ -16,7 +16,6 @@ params {
   max_time = 48.h
 
   // Input data
-  single_end = false
   input_paths = [
     ['test_minigut', ['https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz']],
     ['test_minigut_sample2', ['https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz']]

conf/test_full.config

@@ -6,24 +6,21 @@
  * to run a full size pipeline test. Use as follows:
  *   nextflow run nf-core/mag -profile test_full,<docker/singularity>
  */
-// TODO adjust for full test dataset and specify in .github/workflows/awsfulltest.yml
-// currently this is not used!
 
 params {
   config_profile_name = 'Full test profile'
   config_profile_description = 'Full test dataset to check pipeline function'
 
   // Input data for full size test
-  // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-  // TODO nf-core: Give any required params for the test so that command line flags are not needed
-  single_end = false
-  input_paths = [
-    ['test_minigut', ['https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz']],
-    ['test_minigut_sample2', ['https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz']]
-  ]
-  centrifuge_db = "https://github.com/nf-core/test-datasets/raw/mag/test_data/minigut_cf.tar.gz"
-  kraken2_db = "https://github.com/nf-core/test-datasets/raw/mag/test_data/minigut_kraken.tgz"
-  skip_krona = true
-  min_length_unbinned_contigs = 1
-  max_unbinned_contigs = 2
+  // hg19 reference with highly conserved and low-complexity regions masked by Brian Bushnell
+  host_fasta = "s3://nf-core-awsmegatests/mag/input_data/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
+  manifest = "s3://nf-core-awsmegatests/mag/input_data/manifest.full.txt"
+
+  centrifuge_db = "s3://nf-core-awsmegatests/mag/input_data/p_compressed+h+v.tar.gz"
+  kraken2_db = "s3://nf-core-awsmegatests/mag/input_data/minikraken_8GB_202003.tgz"
+  cat_db = "s3://nf-core-awsmegatests/mag/input_data/CAT_prepare_20200304.tar.gz"
+
+  busco_reference = "s3://nf-core-awsmegatests/mag/input_data/bacteria_odb10.2020-03-06.tar.gz"
+
+  // reproducibility options for megahit and spades not turned on
 }

conf/test_hybrid.config

@@ -16,8 +16,7 @@ params {
   max_time = 48.h
 
   // Input data
-  single_end = false
-  params.manifest = 'https://github.com/nf-core/test-datasets/raw/mag/test_data/manifest.txt'
+  manifest = 'https://github.com/nf-core/test-datasets/raw/mag/test_data/manifest.txt'
   min_length_unbinned_contigs = 1
   max_unbinned_contigs = 2
 }

conf/test_hybrid_host_rm.config

@@ -17,7 +17,7 @@ params {
 
   // Input data
   host_fasta = "https://github.com/nf-core/test-datasets/raw/mag/host_reference/genome.hg38.chr21_10000bp_region.fa"
-  params.manifest = 'https://github.com/nf-core/test-datasets/raw/mag/test_data/manifest_hg38host.txt'
+  manifest = 'https://github.com/nf-core/test-datasets/raw/mag/test_data/manifest_hg38host.txt'
   min_length_unbinned_contigs = 1
   max_unbinned_contigs = 2
 }

containers/busco/Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.2
+FROM nfcore/base:1.11
 LABEL authors="Hadrien Gourlé <hadrien.gourle@slu.se>, Daniel Straub <d4straub@gmail.com>, Sabrina Krakau <sabrinakrakau@gmail.com>" \
       description="Docker image containing BUSCO requirements for the nf-core/mag pipeline"
 
@@ -11,10 +11,10 @@ RUN apt-get update
 RUN apt-get install -y libxt6
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-mag-busco-1.1.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mag-busco-1.1.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-mag-busco-1.1.0 > nf-core-mag-busco-1.1.0.yml
+RUN conda env export --name nf-core-mag-busco-1.1.1 > nf-core-mag-busco-1.1.1.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

containers/busco/environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-mag-busco-1.1.0
+name: nf-core-mag-busco-1.1.1
 channels:
   - conda-forge
   - bioconda