Merge pull request #13 from muneebdev7/test

Test

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# MDL/metabolt: Contributing Guidelines
+# `MDL/metabolt`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving MDL/metabolt.
@@ -13,11 +13,11 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for MDL/metabolt, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [MDL/metabolt issues](https://github.com/MDL/metabolt/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [MDL/metabolt repository](https://github.com/MDL/metabolt) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [muneebdev7/metabolt issues](https://github.com/muneebdev7/metabolt/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this.
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [muneebdev7/metabolt repository](https://github.com/muneebdev7/metabolt) to your GitHub account.
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
-5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged.
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
 
@@ -52,19 +52,19 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Pipeline contribution conventions
 
-To make the MDL/metabolt code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `MDL/metabolt` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -77,7 +77,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
@@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/MDL/metabolt/codespaces)
+- Open the repo in [Codespaces](https://github.com/muneebdev7/metabolt/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,6 +1,7 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+labels:
+  - bug
 body:
 
   - type: textarea

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,6 +1,7 @@
 name: Feature request
 description: Suggest an idea for the MDL/metabolt pipeline
-labels: enhancement
+labels:
+  - enhancement
 body:
   - type: textarea
     id: description

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,11 +11,11 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/MDL/metabolt/tree/master/.github/CONTRIBUTING.md)
 -->
 
-## PR checklist
+# 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/MDL/metabolt/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/muneebdev7/metabolt/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/branch.yml

@@ -1,19 +1,21 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'MDL/metabolt'
+        if: github.repository == 'muneebdev7/metabolt'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == MDL/metabolt ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == muneebdev7/metabolt ]] && [[ $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
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'MDL/metabolt') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'muneebdev7/metabolt') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'MDL/metabolt'
+      github.repository == 'muneebdev7/metabolt'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/MDL/metabolt/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/muneebdev7/metabolt/actions/runs/${{ github.run_id }}) for more details.

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.nf-core.yml

@@ -5,7 +5,12 @@ lint:
   - assets/nf-core-metabolt_logo_light.png
   - docs/images/nf-core-metabolt_logo_light.png
   - docs/images/nf-core-metabolt_logo_dark.png
+  - .github/CONTRIBUTING.md
   - .github/ISSUE_TEMPLATE/config.yml
+  - .github/ISSUE_TEMPLATE/bug_report.yml
+  - .github/ISSUE_TEMPLATE/feature_request.yml
+  - .github/PULL_REQUEST_TEMPLATE.md
+  - .github/workflows/branch.yml
   - .github/workflows/awstest.yml
   - .github/workflows/awsfulltest.yml
   files_unchanged:
@@ -14,6 +19,11 @@ lint:
   - docs/images/nf-core-metabolt_logo_light.png
   - docs/images/nf-core-metabolt_logo_dark.png
   - .github/ISSUE_TEMPLATE/bug_report.yml
+  - .github/ISSUE_TEMPLATE/bug_report.yml
+  - .github/ISSUE_TEMPLATE/feature_request.yml
+  - .github/workflows/branch.yml
+  - .github/CONTRIBUTING.md
+  - .github/PULL_REQUEST_TEMPLATE.md
   multiqc_config:
   - report_comment
   nextflow_config:
@@ -23,11 +33,11 @@ lint:
   - validation.help.afterText
   - validation.summary.beforeText
   - validation.summary.afterText
-nf_core_version: 3.0.2
+nf_core_version: 3.1.1
 org_path: null
 repository_type: pipeline
 template:
-  author: Muneeb
+  author: Muhammad Muneeb Nasir
   description: Lightning fast & automated metagenomic pipeline powered by Nextflow
   force: true
   is_nfcore: false

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json

CITATIONS.md

@@ -25,6 +25,10 @@
 
   > Li, D., Luo, R., Liu, C. M., Leung, C. M., Ting, H. F., Sadakane, K., ... & Lam, T. W. (2016). MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102, 3-11. doi: 10.1016/j.ymeth.2016.02.020.
 
+- [MetaBAT2](https://doi.org/10.7717/peerj.7359)
+
+  > Kang, D. D., Li, F., Kirton, E., Thomas, A., Egan, R., An, H., & Wang, Z. (2019). MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ, 7, e7359. doi: 10.7717/peerj.7359.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
@@ -33,6 +37,12 @@
 
   > Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. doi: 10.1093/bioinformatics/btp352.
 
+## Data
+
+- [Full-size test data](https://doi.org/10.1038/s41467-023-43000-z)
+
+  > Ma, B., Lu, C., Wang, Y. et al. A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources. Nat Commun 14, 7318 (2023). doi.org/10.1038/s41467-023-43000-z
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)