Merge pull request #131 from tillenglert/prepare_release_1.0.0

prepare release 1.0.0

CHANGELOG.md

@@ -3,9 +3,9 @@
 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 - [2022-01-20]
+## v1.0.0 - [2022-01-20]
 
-First release of [nf-core/metapep](https://nf-co.re/metapep/dev), created based on [nf-core](https://nf-co.re) standards and [nf-core/tools](https://nf-co.re/tools) template version 1.13.1.
+First release of [nf-core/metapep](https://nf-co.re/metapep), created based on [nf-core](https://nf-co.re) standards and [nf-core/tools](https://nf-co.re/tools) template version 1.14.1.
 
 ### `Added`
 

assets/methods_description_template.yml

@@ -7,7 +7,7 @@ plot_type: "html"
 data: |
  <h4>Methods</h4>
  <p>Data was processed using nf-core/metapep v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects. Briefly the pipeline uses prodigal (<a href="https://doi.org/10.1186/1471-2105-11-119">Hyatt, D., Chen, GL., LoCascio, P.F. <em>et al.</em>, 2010</a>) to predict proteins from the genomic input files or downloads the proteins from the taxid input directly using Entrez (<a href=https://doi.org/10.1093/nar/gki031">Maglott <em>et al.</em>, 2005</a>). Peptides are generated in discrete lengths from proteins and predicted against chosen alleles using either SYFPEITHI (<a href="https://doi.org/10.1007/s002510050595">Rammensee <em>et al.</em>, 1999</a>), MHCFlurry (<a href="https://doi.org/10.1016/j.cels.2020.06.010">O'Donnel <em>et al.</em>, 2020</a>) or MHCnuggets (<a href="https://doi.org/10.1158/2326-6066.cir-19-0464">Shao <em>et al.</em>, 2019</a>), which are embedded in the epytope framework (<a href="https://doi.org/10.1093/bioinformatics/btw113">Schubert <em>et al.</em>, 2016</a>).
- Resulting epitopeprediction scores distributions and entity binding ratios are plotted using R (<a href="https://www.R-project.org/">R Core Team, 2022</a>). The large amounts of data are handled using a python (<a href="https://www.python.org/">Python Core Team, 2022</a>) framework. All specific software versions and used libraries can be found in the following section and the <a href="https://github.com/nf-core/metapep/blob/dev/CITATIONS.md">CITATIONS.md</a> file.</p>
+ Resulting epitopeprediction scores distributions and entity binding ratios are plotted using R (<a href="https://www.R-project.org/">R Core Team, 2022</a>). The large amounts of data are handled using a python (<a href="https://www.python.org/">Python Core Team, 2022</a>) framework. All specific software versions and used libraries can be found in the following section and the <a href="https://github.com/nf-core/metapep/blob/master/CITATIONS.md">CITATIONS.md</a> file.</p>
  <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
  <pre><code>${workflow.commandLine}</code></pre>
  <p>${tool_citations}</p>

assets/multiqc_config.yml

@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/metapep/
 custom_logo_title: "nf-core/metapep"
 
 report_comment: >
- This report has been generated by the <a href="https://github.com/nf-core/metapep/tree/dev" target="_blank">nf-core/metapep</a>
+ This report has been generated by the <a href="https://github.com/nf-core/metapep/releases/tag/1.0.0" target="_blank">nf-core/metapep</a>
  analysis pipeline. For information about how to interpret these results, please see the
- <a href="https://nf-co.re/metapep/dev/docs/output" target="_blank">documentation</a>.
+ <a href="https://nf-co.re/metapep/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
  "nf-core-metapep-methods-description":
  order: -1000

docs/usage.md

@@ -116,7 +116,7 @@ The pipeline predicts epitopes for specific peptide lengths and for specific all
 nextflow run nf-core/metapep -profile <YOURPROFILE> --outdir <OUTDIR> --show_supported_models
 ```
 
-More on the output can be found at https://nf-co.re/metapep/dev/output#supported-allele-models
+More on the output can be found at https://nf-co.re/metapep/output#supported-allele-models
 
 Moreover, the pipeline checks if a supported prediction model (combination of allele and peptide length) is available if a PSSMs method like SYFPEITHI is chosen and reduces the peptide lengths to a common denominator for further analysis if models are not available.
 

nextflow.config

@@ -267,7 +267,7 @@ manifest {
  description = """From metagenomes to peptides"""
  mainScript = 'main.nf'
  nextflowVersion = '!>=23.04.0'
- version = '1.0dev'
+ version = '1.0.0'
  doi = ''
 }