Merge pull request #302 from nf-core/nf-core-template-merge-2.5.1

Important! Template update for nf-core/tools v2.5.1

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,10 +15,9 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/chip
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/chipseq/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/chipseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/chipseq/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/chipseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -10,7 +10,6 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  CAPSULE_LOG: none
 
 jobs:
   test:
@@ -20,27 +19,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Nextflow versions
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "21.10.3"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
         run: |

.github/workflows/linting.yml

@@ -35,22 +35,48 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
+  PythonBlack:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Check code lints with Black
+        uses: psf/black@stable
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@v3
         with:
-          python-version: "3.6"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies

.nf-core.yml

@@ -1,8 +1 @@
 repository_type: pipeline
-lint:
-  files_unchanged:
-    - .github/workflows/branch.yml
-    - .github/workflows/linting_comment.yml
-    - .github/workflows/linting.yml
-    - .github/PULL_REQUEST_TEMPLATE.md
-    - bin/check_samplesheet.py

CHANGELOG.md

@@ -3,13 +3,13 @@
 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).
 
-## [2.0.0] - 2022-08-11
+## [[2.0.0](https://github.com/nf-core/chipseq/releases/tag/2.0.0)] - 2022-09-30
 
 ### Enhancements & fixes
 
 - Pipeline has been re-implemented in [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
 - All software containers are now exclusively obtained from [Biocontainers](https://biocontainers.pro/#/registry)
-- Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
+- Updated pipeline template to [nf-core/tools 2.5.1](https://github.com/nf-core/tools/releases/tag/2.5.1)
 - [[#128](https://github.com/nf-core/chipseq/issues/128)] - Filter files with no peaks to avoid errors in downstream processes
 - [[#220](https://github.com/nf-core/chipseq/issues/220)] - Fix `phantompeakqualtools` protection stack overflow error
 - [[#233](https://github.com/nf-core/chipseq/issues/233)] - Add `chromap` to the available aligners
@@ -88,7 +88,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 > **NB:** Dependency has been **added** if just the new version information is present.
 > **NB:** Dependency has been **removed** if version information isn't present.
 
-## [1.2.2] - 2021-04-22
+## [[1.2.2](https://github.com/nf-core/chipseq/releases/tag/1.2.2)] - 2021-04-22
 
 - [#206](https://github.com/nf-core/chipseq/issues/206) - Minor patch release to fix Conda environment
 
@@ -97,11 +97,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 - Update r-base `3.6.2` -> `3.6.3`
 - Update r-xfun `0.15` -> `0.20`
 
-## [1.2.1] - 2020-07-29
+## [[1.2.1](https://github.com/nf-core/chipseq/releases/tag/1.2.1)] - 2020-07-29
 
 - [#171](https://github.com/nf-core/chipseq/issues/171) - Minor patch release to update pipeline schema
 
-## [1.2.0] - 2020-07-02
+## [[1.2.0](https://github.com/nf-core/chipseq/releases/tag/1.2.0)] - 2020-07-02
 
 ### `Added`
 
@@ -179,7 +179,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 - Update trim-galore `0.5.0` -> `0.6.5`
 - Update ucsc-bedgraphtobigwig `377` -> `357`
 
-## [1.1.0] - 2019-11-05
+## [[1.1.0](https://github.com/nf-core/chipseq/releases/tag/1.1.0)] - 2019-11-05
 
 ### `Added`
 
@@ -228,7 +228,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | `--skipIGV`                  | `--skip_igv`              |
 | `--skipMultiQC`              | `--skip_multiqc`          |
 
-## [1.0.0] - 2019-06-06
+## [[1.0.0](https://github.com/nf-core/chipseq/releases/tag/1.0.0)] - 2019-06-06
 
 Initial release of nf-core/chipseq pipeline.
 

CITATION.cff

@@ -0,0 +1,56 @@
+cff-version: 1.2.0
+message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
+authors:
+  - family-names: Ewels
+    given-names: Philip
+  - family-names: Peltzer
+    given-names: Alexander
+  - family-names: Fillinger
+    given-names: Sven
+  - family-names: Patel
+    given-names: Harshil
+  - family-names: Alneberg
+    given-names: Johannes
+  - family-names: Wilm
+    given-names: Andreas
+  - family-names: Ulysse Garcia
+    given-names: Maxime
+  - family-names: Di Tommaso
+    given-names: Paolo
+  - family-names: Nahnsen
+    given-names: Sven
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Ewels
+      given-names: Philip
+    - family-names: Peltzer
+      given-names: Alexander
+    - family-names: Fillinger
+      given-names: Sven
+    - family-names: Patel
+      given-names: Harshil
+    - family-names: Alneberg
+      given-names: Johannes
+    - family-names: Wilm
+      given-names: Andreas
+    - family-names: Ulysse Garcia
+      given-names: Maxime
+    - family-names: Di Tommaso
+      given-names: Paolo
+    - family-names: Nahnsen
+      given-names: Sven
+  doi: 10.1038/s41587-020-0439-x
+  journal: nature biotechnology
+  start: 276
+  end: 278
+  title: "The nf-core framework for community-curated bioinformatics pipelines."
+  issue: 3
+  volume: 38
+  year: 2020
+  url: https://dx.doi.org/10.1038/s41587-020-0439-x

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Philip Ewels, Jose Espinosa-Carrasco, Harshil Patel
+Copyright (c) Espinosa-Carrasco J, Patel H, Wang C, Ewels P
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,19 +1,14 @@
 # ![nf-core/chipseq](docs/images/nf-core-chipseq_logo_light.png#gh-light-mode-only) ![nf-core/chipseq](docs/images/nf-core-chipseq_logo_dark.png#gh-dark-mode-only)
 
-[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/chipseq/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/chipseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/chipseq/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.-1073c8)](https://doi.org/10.5281/zenodo.3240506)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3240506-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3240506)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
-[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
-[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/chipseq)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23chipseq-4A154B?logo=slack)](https://nfcore.slack.com/channels/chipseq)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
-[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23chipseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/chipseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 

assets/email_template.txt

@@ -6,7 +6,6 @@
                                         `._,._,'
   nf-core/chipseq v${version}
 ----------------------------------------------------
-
 Run Name: $runName
 
 <% if (success){