Merge pull request nf-core#113 from drpatelh/master

Update docs, CI, README and environment
IanKouzel · Jun 30, 2020 · 36a427d · 36a427d
2 parents 9245dbf + 9f1a5fe
commit 36a427d
Show file tree

Hide file tree

Showing 27 changed files with 476 additions and 393 deletions.
diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
@@ -1,5 +1,9 @@
-# Markdownlint configuration file
-default: true,
-line-length: false
-no-duplicate-header:
-    siblings_only: true
+# Markdownlint configuration file
+default: true,
+line-length: false
+no-duplicate-header:
+    siblings_only: true
+MD033:
+    allowed_elements: [details, summary, p, img]
+MD007:
+    indent: 4
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,50 +1,125 @@
 name: nf-core CI
-# This workflow is triggered on pushes and PRs to the repository.
+# This workflow is triggered on releases and pull-requests.
 # It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
 
 jobs:
   test:
+    name: Run workflow tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}
+    runs-on: ubuntu-latest
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
         nxf_ver: ['19.10.0', '']
     steps:
-      - uses: actions/checkout@v2
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/atacseq:dev
+
       - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/atacseq:dev
           docker tag nfcore/atacseq:dev nfcore/atacseq:dev
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
   parameters:
+    name: Test workflow parameters
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}
+    runs-on: ubuntu-latest
     env:
       NXF_VER: '19.10.0'
       NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         parameters: [--single_end, --skip_trimming, --skip_merge_replicates, --skip_consensus_peaks]
     steps:
-      - uses: actions/checkout@v2
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v1
+        with:
+          PREFIX_FILTER: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.GIT_DIFF
+        run: docker build --no-cache . -t nfcore/atacseq:dev
+
       - name: Pull docker image
+        if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/atacseq:dev
           docker tag nfcore/atacseq:dev nfcore/atacseq:dev
-      - name: Run pipeline with various options
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with various parameters
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+
+  push_dockerhub:
+    name: Push new Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    # Only run if the tests passed
+    needs: test
+    # Only run for the nf-core repo, for releases and merged PRs
+    if: ${{ github.repository == 'nf-core/atacseq' && (github.event_name == 'release' || github.event_name == 'push') }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Build new docker image
+        run: docker build --no-cache . -t nfcore/atacseq:latest
+
+      - name: Push Docker image to DockerHub (dev)
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker tag nfcore/atacseq:latest nfcore/atacseq:dev
+          docker push nfcore/atacseq:dev
+
+      - name: Push Docker image to DockerHub (release)
+        if: ${{ github.event_name == 'release' }}
+        run: |
+          echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
+          docker push nfcore/atacseq:latest
+          docker tag nfcore/atacseq:latest nfcore/atacseq:${{ github.event.release.tag_name }}
+          docker push nfcore/atacseq:${{ github.event.release.tag_name }}
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -33,18 +33,29 @@ jobs:
   nf-core:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
       - 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 dependencies
         run: |
           python -m pip install --upgrade pip
           pip install nf-core
+
       - name: Run nf-core lint
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core lint ${GITHUB_WORKSPACE}
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,22 +19,22 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Replace `set` with `tuple` and `file()` with `path()` in all processes
 * Capitalise process names
 * Parameters:
-  * `--skip_peak_qc` to skip MACS2 peak QC plot generation
-  * `--skip_peak_annotation` to skip annotation of MACS2 and consensus peaks with HOMER
-  * `--skip_consensus_peaks` to skip consensus peak generation
-  * `--deseq2_vst` to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
-  * `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)
+    * `--skip_peak_qc` to skip MACS2 peak QC plot generation
+    * `--skip_peak_annotation` to skip annotation of MACS2 and consensus peaks with HOMER
+    * `--skip_consensus_peaks` to skip consensus peak generation
+    * `--deseq2_vst` to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
+    * `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)
 
 ### `Fixed`
 
 * [#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
 * [#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script
 * [#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r
+* [#110](https://github.com/nf-core/atacseq/pull/110) - updated AWS test GitHub actions
 * [nf-core/chipseq#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
 * [nf-core/chipseq#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
 * [nf-core/chipseq#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped
 * Make executables in `bin/` compatible with Python 3
-* [#110](https://github.com/nf-core/atacseq/pull/110) - updated AWS test GitHub actions
 
 ### `Dependencies`
 
@@ -49,24 +49,24 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Update gawk `4.2.1` -> `5.1.0`
 * Update r-base `3.4.1` -> `3.6.2`
 * Update r-optparse `1.6.0` -> `1.6.6`
-* Update r-ggplot2 `3.1.0` -> `3.3.0`
+* Update r-ggplot2 `3.1.0` -> `3.3.2`
 * Update r-pheatmap `1.0.10` -> `1.0.12`
 * Update r-lattice `0.20_35` -> `0.20_41`
 * Update r-upsetr `1.3.3` -> `1.4.0`
 * Update r-scales `1.0.0` -> `1.1.1`  
-* Update r-xfun `0.3` -> `0.14`
+* Update r-xfun `0.3` -> `0.15`
 * Update fastqc `0.11.8` -> `0.11.9`
 * Update trim-galore `0.5.0` -> `0.6.5`
 * Update samtools `1.9` -> `1.10`
-* Update picard `2.19.0` -> `2.22.8`
+* Update picard `2.19.0` -> `2.23.1`
 * Update pysam `0.15.2` -> `0.15.3`
 * Update bedtools `2.27.1` -> `2.29.2`
 * Update ucsc-bedgraphtobigwig `377` -> `357`
 * Update deeptools `3.2.1` -> `3.4.3`
 * Update macs2 `2.1.2` -> `2.2.7.1`
 * Update homer `4.9.1` -> `4.11`
 * Update ataqv `1.0.0` -> `1.1.1`
-* Update subread `1.6.4` -> `2.0.0`
+* Update subread `1.6.4` -> `2.0.1`
 * Update multiqc `1.7` -> `1.8`
 * Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
 * Update bioconductor-vsn `3.46.0` -> `3.54.0`
@@ -83,14 +83,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Add `CITATIONS.md` file
 * Capitalised process names
 * Add parameters:
-  * `--seq_center`
-  * `--trim_nextseq`
-  * `--fingerprint_bins`
-  * `--broad_cutoff`
-  * `--min_reps_consensus`
-  * `--save_macs_pileup`
-  * `--skip_diff_analysis`
-  * `--skip_*` for skipping QC steps
+    * `--seq_center`
+    * `--trim_nextseq`
+    * `--fingerprint_bins`
+    * `--broad_cutoff`
+    * `--min_reps_consensus`
+    * `--save_macs_pileup`
+    * `--skip_diff_analysis`
+    * `--skip_*` for skipping QC steps
 
 ### `Fixed`
 

diff --git a/README.md b/README.md
@@ -3,10 +3,11 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/atacseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/atacseq/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/atacseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/atacseq/actions)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2634132.svg)](https://doi.org/10.5281/zenodo.2634132)
 
 [![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/atacseq.svg)](https://hub.docker.com/r/nfcore/atacseq)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2634132.svg)](https://doi.org/10.5281/zenodo.2634132)
+![[Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23atacseq-4A154B?logo=slack)](https://nfcore.slack.com/channels/atacseq)
 
 ## Introduction
 
@@ -59,23 +60,23 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-i. Install [`nextflow`](https://nf-co.re/usage/installation)
+1. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-ii. 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 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))_
 
-iii. Download the pipeline and test it on a minimal dataset with a single command
+3. Download the pipeline and test it on a minimal dataset with a single command:
 
-```bash
-nextflow run nf-core/atacseq -profile test,<docker/singularity/conda/institute>
-```
+    ```bash
+    nextflow run nf-core/atacseq -profile test,<docker/singularity/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.
+    > 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.
 
-iv. Start running your own analysis!
+4. Start running your own analysis!
 
-```bash
-nextflow run nf-core/atacseq -profile <docker/singularity/conda/institute> --input design.csv --genome GRCh37
-```
+    ```bash
+    nextflow run nf-core/atacseq -profile <docker/singularity/conda/institute> --input design.csv --genome GRCh37
+    ```
 
 See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
 
@@ -98,20 +99,20 @@ The pipeline was originally written by [The Bioinformatics & Biostatistics Group
 
 The pipeline was developed by [Harshil Patel](mailto:harshil.patel@crick.ac.uk).
 
-The [nf-core/rnaseq](https://github.com/nf-core/rnaseq) and [nf-core/chipseq](https://github.com/nf-core/chipseq) pipelines developed by Phil Ewels were initially used as a template for this pipeline. Many thanks to Phil for all of his help and advice, and the team at SciLifeLab.
-
-Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@crickbabs](https://github.com/crickbabs), [drewjbeh](https://github.com/drewjbeh), [@houghtos](https://github.com/houghtos), [@jinmingda](https://github.com/jinmingda), [@ktrns](https://github.com/ktrns), [@MaxUlysse](https://github.com/MaxUlysse), [@mashehu](https://github.com/mashehu), [@micans](https://github.com/micans), [@pditommaso](https://github.com/pditommaso) and [@sven1103](https://github.com/sven1103).
+Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@ewels](https://github.com/ewels), [@apeltzer](https://github.com/apeltzer), [@crickbabs](https://github.com/crickbabs), [drewjbeh](https://github.com/drewjbeh), [@houghtos](https://github.com/houghtos), [@jinmingda](https://github.com/jinmingda), [@ktrns](https://github.com/ktrns), [@MaxUlysse](https://github.com/MaxUlysse), [@mashehu](https://github.com/mashehu), [@micans](https://github.com/micans), [@pditommaso](https://github.com/pditommaso) and [@sven1103](https://github.com/sven1103).
 
 ## Contributions and Support
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/atacseq) (you can join with [this invite](https://nf-co.re/join/slack)).
+For further information or help, don't hesitate to get in touch on the [Slack `#atacseq` channel](https://nfcore.slack.com/channels/atacseq) (you can join with [this invite](https://nf-co.re/join/slack)).
 
 ## Citation
 
 If you use nf-core/atacseq for your analysis, please cite it using the following doi: [10.5281/zenodo.2634132](https://doi.org/10.5281/zenodo.2634132)
 
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+
 You can cite the `nf-core` publication as follows:
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
@@ -120,5 +121,3 @@ You can cite the `nf-core` publication as follows:
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).  
 > ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
-
-An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -13,7 +13,7 @@ params {
 
   // Input data
   input = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design_full.csv'
-  
+
   // Genome references
-  genome = 'hg19'
+  genome = 'hg38'
 }
diff --git a/docs/images/mqc_annotatePeaks_feature_percentage_plot.png b/docs/images/mqc_annotatePeaks_feature_percentage_plot.png
diff --git a/docs/images/mqc_cutadapt_plot.png b/docs/images/mqc_cutadapt_plot.png
diff --git a/docs/images/mqc_deeptools_plotFingerprint_plot.png b/docs/images/mqc_deeptools_plotFingerprint_plot.png
diff --git a/docs/images/mqc_deeptools_plotProfile_plot.png b/docs/images/mqc_deeptools_plotProfile_plot.png
diff --git a/docs/images/mqc_deseq2_pca_plot.png b/docs/images/mqc_deseq2_pca_plot.png
diff --git a/docs/images/mqc_deseq2_sample_similarity_plot.png b/docs/images/mqc_deseq2_sample_similarity_plot.png
diff --git a/docs/images/mqc_featureCounts_assignment_plot.png b/docs/images/mqc_featureCounts_assignment_plot.png
diff --git a/docs/images/mqc_frip_score_plot.png b/docs/images/mqc_frip_score_plot.png
diff --git a/docs/images/mqc_macs2_peak_count_plot.png b/docs/images/mqc_macs2_peak_count_plot.png
diff --git a/docs/images/mqc_picard_deduplication_plot.png b/docs/images/mqc_picard_deduplication_plot.png
diff --git a/docs/images/mqc_picard_insert_size_plot.png b/docs/images/mqc_picard_insert_size_plot.png
diff --git a/docs/images/mqc_preseq_plot.png b/docs/images/mqc_preseq_plot.png
diff --git a/docs/images/mqc_samtools_idxstats_plot.png b/docs/images/mqc_samtools_idxstats_plot.png
diff --git a/docs/images/mqc_samtools_stats_plot.png b/docs/images/mqc_samtools_stats_plot.png
diff --git a/docs/images/r_deseq2_ma_plot.png b/docs/images/r_deseq2_ma_plot.png
diff --git a/docs/images/r_deseq2_volcano_plot.png b/docs/images/r_deseq2_volcano_plot.png