Remove nf core branding

.github/CONTRIBUTING.md

@@ -9,10 +9,6 @@ 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:
@@ -50,13 +46,13 @@ 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 [nf-core/staramr documentation](https://github.com/phac-nml/staramrnf).
 
 ## Pipeline contribution conventions
 
@@ -85,7 +81,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
 

.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/nf-core-staramr/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.

README.md

@@ -1,106 +1,89 @@
-# ![nf-core/staramr](docs/images/nf-core-staramr_logo_light.png#gh-light-mode-only) ![nf-core/staramr](docs/images/nf-core-staramr_logo_dark.png#gh-dark-mode-only)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A523.04.3-brightgreen.svg)](https://www.nextflow.io/)
 
-[![GitHub Actions CI Status](https://github.com/nf-core/staramr/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/staramr/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/staramr/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/staramr/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/staramr/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%A523.04.0-23aa62.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/staramr)
-
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23staramr-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/staramr)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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)
+# `staramr`: nextflow pipeline
 
 ## Introduction
 
-**nf-core/staramr** is a bioinformatics pipeline that ...
+**staramr: nextflow pipeline** is the nextflow adaptation of the [staramr](https://github.com/phac-nml/staramr/)
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
-
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+> `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.
 
 ## Usage
 
-:::note
 If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
 to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
 with `-profile test` before running the workflow on actual data.
-:::
-
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
 
-First, prepare a samplesheet with your input data that looks as follows:
-
-`samplesheet.csv`:
-
-```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+```bash
+ nextflow run main.nf -profile test,docker --outdir ./results
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+### Input
+
+The input to the pipeline is a standard sample sheet (passed as `--input samplesheet.csv`) that looks like:
 
--->
+| sample  | contigs          | species             |
+| ------- | ---------------- | ------------------- |
+| SampleA | genomeA.fastq.gz | Salmonella enterica |
 
-Now, you can run the pipeline using:
+The structure of this file is defined in [assets/schema_input.json](assets/schema_input.json). Validation of the sample sheet is performed by [nf-validation](https://nextflow-io.github.io/nf-validation/).
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
+### Output
 
 ```bash
-nextflow run nf-core/staramr \
-   -profile <docker/singularity/.../institute> \
-   --input samplesheet.csv \
-   --outdir <OUTDIR>
+results/staramr/
+└── SampleA_results
+    ├── detailed_summary.tsv
+    ├── mlst.tsv
+    ├── plasmidfinder.tsv
+    ├── resfinder.tsv
+    ├── results.xlsx
+    ├── settings.txt
+    └── summary.tsv
 ```
 
-:::warning
-Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
-:::
+See the [staramr documentation](https://github.com/phac-nml/staramr/blob/development/README.md) for more details and explanations.
 
-For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/staramr/usage) and the [parameter documentation](https://nf-co.re/staramr/parameters).
+## Citation
 
-## Pipeline output
+### staramr
 
-To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/staramr/results) tab on the nf-core website pipeline page.
-For more details about the output files and reports, please refer to the
-[output documentation](https://nf-co.re/staramr/output).
+> Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, Kearney A, Nadon C, Mabon P, Thiessen J, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Domselaar GV, Reid-Smith RJ, Mulvey MR. **Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr**. Microorganisms. 2022; 10(2):292. https://doi.org/10.3390/microorganisms10020292
 
-## Credits
+### Databases used by staramr
 
-nf-core/staramr was originally written by Eric Marinier.
+> **Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV**. 2012. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67:2640–2644. doi: [10.1093/jac/dks261][resfinder-cite]
 
-We thank the following people for their extensive assistance in the development of this pipeline:
+> **Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O, Aarestrup F**. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother. 2017; 72(10): 2764–8. doi: [10.1093/jac/dkx217][pointfinder-cite]
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+> **Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H**. PlasmidFinder and pMLST: in silico detection and typing of plasmids. Antimicrob. Agents Chemother. 2014. April 28th. doi: [10.1128/AAC.02412-14][plasmidfinder-cite]
 
-## Contributions and Support
+> **Seemann T**, MLST Github https://github.com/tseemann/mlst
 
-If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+> **Jolley KA, Bray JE and Maiden MCJ**. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications [version 1; peer review: 2 approved]. Wellcome Open Res 2018, 3:124. doi: [10.12688/wellcomeopenres.14826.1][mlst-cite]
 
-For further information or help, don't hesitate to get in touch on the [Slack `#staramr` channel](https://nfcore.slack.com/channels/staramr) (you can join with [this invite](https://nf-co.re/join/slack)).
+### nf-core
 
-## Citations
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/staramr for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+> The nf-core framework for community-curated bioinformatics pipelines.
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
+> In addition, references of tools and data used in this pipeline are as follows:
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+## Legal
 
-An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+Copyright 2024 Government of Canada
 
-You can cite the `nf-core` publication as follows:
+Licensed under the MIT License (the "License"); you may not use
+this work except in compliance with the License. You may obtain a copy of the
+License at:
 
-> **The nf-core framework for community-curated bioinformatics pipelines.**
->
-> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
->
-> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+https://opensource.org/license/mit/
+
+Unless required by applicable law or agreed to in writing, software distributed
+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.

assets/methods_description_template.yml

@@ -1,4 +1,4 @@
-id: "nf-core-staramr-methods-description"
+id: "staramrnf-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
 section_name: "nf-core/staramr Methods Description"
 section_href: "https://github.com/nf-core/staramr"

assets/multiqc_config.yml

@@ -3,11 +3,11 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/staramr/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
-  "nf-core-staramr-methods-description":
+  "staramrnf-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "nf-core-staramr-summary":
+  "staramrnf-summary":
     order: -1002
 
 export_plots: true

assets/sendmail_template.txt

@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="nf-core-staramr_logo.png"
+Content-Type: image/png;name="staramrnf_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="nf-core-staramr_logo_light.png"
+Content-Disposition: inline; filename="staramrnf_logo_light.png"
 
-<% out << new File("$projectDir/assets/nf-core-staramr_logo_light.png").
+<% out << new File("$projectDir/assets/staramrnf_logo_light.png").
     bytes.
     encodeBase64().
     toString().

conf/test.config

@@ -20,5 +20,5 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "https://github.com/phac-nml/nf-core-staramr/raw/dev/assets/samplesheet.csv"
+    input = "https://github.com/phac-nml/staramrnf/raw/dev/assets/samplesheet.csv"
 }