nf-core · nf-core-bot · Mar 24, 2022 · May 16, 2022 · Aug 30, 2022 · Sep 1, 2022
diff --git a/.editorconfig b/.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

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/circ
 
 - [ ] 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/circdna/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/circdna _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/circdna/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/circdna _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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -28,6 +28,3 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/circdna/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -23,6 +23,3 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/circdna/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/circdna'
         run: |
-          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/circdna ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/circdna ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
@@ -42,4 +42,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-#
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -10,7 +10,6 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  CAPSULE_LOG: none
 
 jobs:
   test:
@@ -20,33 +19,21 @@ 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
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-#
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -0,0 +1,55 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/circdna'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push
diff --git a/.github/workflows/linting.yml b/.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@v1
+      - uses: actions/setup-python@v3
         with:
-          python-version: "3.6"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies
@@ -78,5 +104,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-
-#
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -26,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-#
diff --git a/.prettierignore b/.prettierignore
@@ -0,0 +1,9 @@
+email_template.html
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v1.0dev - [date]
+## v1.0.2dev - [date]
 
 Initial release of nf-core/circdna, created with the [nf-core](https://nf-co.re/) template.
 

diff --git a/CITATION.cff b/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
diff --git a/README.md b/README.md
@@ -1,51 +1,33 @@
-# ![nf-core/circdna](docs/images/nf-core/circdna_logo_light.png#gh-light-mode-only) ![nf-core/circdna](docs/images/nf-core/circdna_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/circdna](docs/images/nf-core-circdna_logo_light.png#gh-light-mode-only) ![nf-core/circdna](docs/images/nf-core-circdna_logo_dark.png#gh-dark-mode-only)
 
-[![GitHub Actions CI Status](https://github.com/nf-core/circdna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circdna/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/circdna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circdna/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circdna/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circdna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![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?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/circdna)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circdna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circdna)
-[![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)
-
-## IMPORTANT
-
-AmpliconArchitect is currently only runnable using **conda**. Please specify -profile conda, when using AmpliconArchitect.
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circdna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circdna)[![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
 
-**nf-core/circdna** is a bioinformatics best-practice analysis pipeline for the identification of extrachromosomal circular DNAs (ecDNAs) with short read sequencing data.
+<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
+
+**nf-core/circdna** is a bioinformatics best-practice analysis pipeline for Pipeline for the identification of circular DNAs.
 
 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 uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
 <!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
 
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/circdna/results).
+On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/circdna/results).
 
 ## Pipeline summary
 
-1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
-2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
-4. Map reads using BWA-MEM ([`BWA`](https://github.com/lh3/bwa))
-5. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
-6. Choice of multiple Circular DNA identification routes
-   1. [`Circle-Map ReadExtractor`](https://github.com/iprada/Circle-Map) -> [`Circle-Map Realign`](https://github.com/iprada/Circle-Map)
-   2. [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/)
-   3. [`Samblaster`](https://github.com/GregoryFaust/samblaster) -> [`Circle_finder`](https://github.com/pk7zuva/Circle_finder)
-   4. Identification of amplified ecDNAs [`AmpliconArchitect`](https://github.com/virajbdeshpande/AmpliconArchitect)
-   5. DeNovo Assembly of ecDNAs [`Unicycler`](https://github.com/rrwick/Unicycler) -> [`Minimap2`](https://github.com/lh3/minimap2)
-7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-## Overview
-
-![nf-core/circdna/metromap](docs/images/circdna_pipeline_metromap.png)
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Quick Start
 
@@ -55,7 +37,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```console
+   ```bash
    nextflow run nf-core/circdna -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 
@@ -68,7 +50,9 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 4. Start running your own analysis!
 
-   ```console
+   <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
+
+   ```bash
    nextflow run nf-core/circdna --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
@@ -78,13 +62,11 @@ The nf-core/circdna pipeline comes with documentation about the pipeline [usage]
 
 ## Credits
 
-Main authors:
-
-- [Daniel Schreyer](https://github.com/DSchreyer), University of Glasgow, Institute of Cancer Sciences, Peter Bailey Lab
+nf-core/circdna was originally written by Daniel Schreyer.
 
-### Funding
+We thank the following people for their extensive assistance in the development of this pipeline:
 
-Daniel Schreyer received funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie grant agreement No 861196 designated for PRECODE.
+<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
 
 ## Contributions and Support