Merge pull request #23 from phac-nml/dev

0.1.0 Release

.editorconfig

@@ -22,3 +22,15 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset
+
+# ignore test staramr tsv files with empty columns
+[tests/data/*]
+trim_trailing_whitespace = false

.github/CONTRIBUTING.md

@@ -1,24 +1,20 @@
-# nf-core/staramr: Contributing Guidelines
+# phac-nml/staramrnf: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/staramr.
+Many thanks for taking an interest in improving phac-nml/staramrnf.
 
-We try to manage the required tasks for nf-core/staramr using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for phac-nml/staramrnf using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/staramr then the best place to ask is on the nf-core Slack [#staramr](https://nfcore.slack.com/channels/staramr) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
-
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/staramr, the standard workflow is as follows:
+If you'd like to write some code for phac-nml/staramrnf, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/staramr issues](https://github.com/nf-core/staramr/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 [nf-core/staramr repository](https://github.com/nf-core/staramr) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [phac-nml/staramrnf issues](https://github.com/phac-nml/staramrnf/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 [phac-nml/staramrnf repository](https://github.com/phac-nml/staramrnf) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core 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
@@ -50,17 +46,17 @@ 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`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- A PR should be made on `main` from patch to directly this particular bug.
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/staramr documentation](https://nf-co.re/staramr/usage) and don't hesitate to get in touch on the nf-core Slack [#staramr](https://nfcore.slack.com/channels/staramr) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [phac-nml/staramrnf documentation](https://github.com/phac-nml/staramrnf).
 
 ## Pipeline contribution conventions
 
-To make the nf-core/staramr 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 phac-nml/staramrnf 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
 
@@ -110,7 +106,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/staramr/codespaces)
+- Open the repo in [Codespaces](https://github.com/phac-nml/staramrnf/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/staramr pipeline documentation](https://nf-co.re/staramr/usage)
+        - [phac-nml/staramrnf pipeline documentation](https://github.com/phac-nml/staramrnf/blob/main/docs/usage.md)
 
   - type: textarea
     id: description
@@ -47,4 +47,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/staramr _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of phac-nml/staramrnf _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,7 +1,4 @@
 contact_links:
-  - name: Join nf-core
-    url: https://nf-co.re/join
-    about: Please join the nf-core community here
-  - name: "Slack #staramr channel"
-    url: https://nfcore.slack.com/channels/staramr
-    about: Discussion about the nf-core/staramr pipeline
+  - name: "GitHub"
+    url: https://github.com/phac-nml/staramrnf
+    about: The GitHub page for development.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/staramr pipeline
+description: Suggest an idea for the phac-nml/staramrnf pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,21 @@
 <!--
-# nf-core/staramr pull request
+# staramr: nextflow pipeline pull request
 
-Many thanks for contributing to nf-core/staramr!
+Many thanks for contributing to staramr: nextflow pipeline!
 
 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/staramr/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/phac-nml/staramrnf/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## 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/staramr/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/staramr _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/phac-nml/staramrnf/tree/main/.github/CONTRIBUTING.md)
 - [ ] 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.

.nf-core.yml

@@ -1 +1,38 @@
 repository_type: pipeline
+nf_core_version: "2.14.1"
+lint:
+  files_exist:
+    - assets/nf-core-staramr_logo_light.png
+    - docs/images/nf-core-staramr_logo_light.png
+    - docs/images/nf-core-staramr_logo_dark.png
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - lib/Utils.groovy
+    - lib/WorkflowMain.groovy
+    - lib/NfcoreTemplate.groovy
+    - lib/WorkflowStaramr.groovy
+  files_unchanged:
+    - assets/sendmail_template.txt
+    - assets/email_template.html
+    - lib/NfcoreTemplate.groovy
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - assets/email_template.txt
+    - docs/README.md
+    - LICENSE
+    - .gitignore
+  pipeline_name_conventions: False
+  actions_awsfulltest: False
+  multiqc_config:
+    - report_comment
+  nextflow_config:
+    - custom_config
+    - manifest.name
+    - manifest.homePage
+  readme:
+    - nextflow_badge
+
+template:
+  prefix: phac-nml

.pre-commit-config.yaml

@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

.prettierignore

@@ -9,4 +9,4 @@ results/
 testing/
 testing*
 *.pyc
-bin/
+tests/data/*

CHANGELOG.md

@@ -1,16 +1,18 @@
-# nf-core/staramr: Changelog
+# phac-nml/staramrnf: 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).
 
-## v1.0dev - [date]
+## [0.1.0] - 2024-08-14
 
-Initial release of nf-core/staramr, created with the [nf-core](https://nf-co.re/) template.
+Initial release of staramrnf, or staramr nextflow pipeline, is a nextflow wrapper of [staramr](https://github.com/phac-nml/staramr/).
 
-### `Added`
+`staramr` (_AMR) scans bacterial genome contigs against the [ResFinder][resfinder-db], [PointFinder][pointfinder-db], and [PlasmidFinder][plasmidfinder-db] databases (used by the [ResFinder webservice][resfinder-web] and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The `star|_`in`staramr` indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases.
 
-### `Fixed`
+staramrnf follows the `nf-core` pipeline file structure and used the nf-core [template](https://nf-co.re/docs/contributing/pipelines/pipeline_file_structure)
 
-### `Dependencies`
-
-### `Deprecated`
+[resfinder-db]: https://bitbucket.org/genomicepidemiology/resfinder_db
+[pointfinder-db]: https://bitbucket.org/genomicepidemiology/pointfinder_db
+[plasmidfinder-db]: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
+[resfinder-web]: http://genepi.food.dtu.dk/resfinder
+[0.1.0]: https://github.com/phac-nml/staramrnf/releases/tag/0.1.0

CITATIONS.md

@@ -1,4 +1,4 @@
-# nf-core/staramr: Citations
+# phac-nml/staramrnf: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
@@ -10,7 +10,6 @@
 
 ## Pipeline tools
 
-
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)