Nfcore and structuring modules for collaboration

.dockerignore

@@ -20,3 +20,4 @@ Autometa.egg-info
 # Ignore databases
 autometa/databases
 !autometa/databases/markers
+/work

.editorconfig

@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{yml,yaml}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset

.gitattribute

@@ -0,0 +1 @@
+*.config linguist-language=nextflow

.gitattributes

@@ -0,0 +1 @@
+*.config linguist-language=nextflow

.github/.dockstore.yml

@@ -0,0 +1,6 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config
+    publish: True

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #autometa channel"
+    url: https://nfcore.slack.com/channels/autometa
+    about: Discussion about the nf-core/autometa pipeline

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,26 @@
+<!--
+# nf-core/autometa pull request
+
+Many thanks for contributing to nf-core/autometa!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
+
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/autometa/tree/master/.github/CONTRIBUTING.md)
+-->
+<!-- markdownlint-disable ul-indent -->
+
+## PR checklist
+
+- [ ] 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/autometa/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/autometa _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`).
+- [ ] Usage Documentation in `docs/usage.md` is updated.
+- [ ] Output Documentation in `docs/output.md` is updated.
+- [ ] `CHANGELOG.md` is updated.
+- [ ] `README.md` is updated (including new tool citations and authors/contributors).

.github/workflows/ci.yml

@@ -0,0 +1,41 @@
+name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
+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_TODO' }}
+    runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ["21.04.0", ""]
+    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/
+
+      - name: Run pipeline with test data
+        run: |
+          docker build . -t jason-c-kwan/autometa:test
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --autometa_image_tag 'latest'

.github/workflows/linting.yml

@@ -0,0 +1,52 @@
+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:
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  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: 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 -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Save PR number
+        if: ${{ always() }}
+        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
+
+      - name: Upload linting log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: linting-logs
+          path: |
+            lint_log.txt
+            lint_results.md
+            PR_number.txt

.github/workflows/linting_comment.yml

@@ -0,0 +1,27 @@
+name: nf-core linting comment
+# This workflow is triggered after the linting action is complete
+# It posts an automated comment to the PR, even if the PR is coming from a fork
+
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download lint results
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          workflow: linting.yml
+
+      - name: Get PR number
+        id: pr_number
+        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+
+      - name: Post PR comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.pr_number.outputs.pr_number }}
+          path: linting-logs/lint_results.md

.gitignore

@@ -16,7 +16,7 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
+!nextflow/lib/
 lib64/
 parts/
 sdist/
@@ -156,7 +156,12 @@ tests/data/*
 .DS_Store
 
 # nextflow
-.nextflow
-.nextflow.log*
+.nextflow*
 pipeline_info
-work
+work/
+large_db/
+nf-params.json
+autometa_interim_dir/
+autometa_outdir/
+autometa_tracedir/
+

.markdownlint.yml

@@ -0,0 +1,14 @@
+# Markdownlint configuration file
+default: true
+line-length: false
+ul-indent:
+    indent: 4
+no-duplicate-header:
+    siblings_only: true
+no-inline-html:
+    allowed_elements:
+        - img
+        - p
+        - kbd
+        - details
+        - summary

.nf-core.yml

@@ -0,0 +1,26 @@
+lint:
+  files_exist:
+    - .github/workflows/branch.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - .travis.yml
+    - docs/usage.md
+    - docs/output.md
+
+  files_unchanged:
+    - manifest
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.md
+    - .github/ISSUE_TEMPLATE/feature_request.md
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - bin/scrape_software_versions.py
+    - docs/README.md
+    - .gitignore
+    - LICENSE
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - lib/NfcoreTemplate.groovy
+  template_strings: false
+  nextflow_config: false

CHANGELOG.md

@@ -0,0 +1,16 @@
+# nf-core/autometa: Changelog
+
+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).
+
+## v2.0.0 - [date]
+
+Second release of nf-core/autometa, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`

CITATIONS.md

@@ -0,0 +1,48 @@
+# Autometa: 
+
+## [Autometa](https://github.com/KwanLab/Autometa)
+    > Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Research, 2019. DOI: https://doi.org/10.1093/nar/gkz148
+
+## [python](https://www.python.org)
+    > Van Rossum, G., & Drake, F. L. (2009). Python 3 Reference Manual. Scotts Valley, CA: CreateSpace.
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
+
+* [Diamond](https://github.com/bbuchfink/diamond)
+    > Buchfink B, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18, 366–368 (2021). doi:10.1038/s41592-021-01101-x
+
+* [HMMER](http://hmmer.org)
+    > HMMER Web Server: Interactive Sequence Similarity Searching. R. D. Finn, J. Clements, S. R. Eddy. Nucleic Acids Research, 39:W29-37, 2011.
+
+* [Prodigal](https://github.com/hyattpd/Prodigal)
+    > Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). https://doi.org/10.1186/1471-2105-11-119
+
+* [Samtools](http://www.htslib.org)
+    > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H, Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2) giab008 [https://pubmed.ncbi.nlm.nih.gov/33590861]
+
+* [SeqKit](https://github.com/shenwei356/seqkit)
+    > W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.
+
+## Software packaging/containerisation tools
+
+* [Anaconda](https://anaconda.com)
+    > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+    > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+
+* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+    > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.