Merge pull request #8 from FriederikeHanssen/reviewcomments

adress reviews

.github/PULL_REQUEST_TEMPLATE.md

@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/qbic-pipelin
 - [ ] 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/qbic-pipelines/vcftomaf/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] 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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

CHANGELOG.md

@@ -3,6 +3,6 @@
 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).
 
-## v1.0.0 - 12-03-2024
+## v1.0.0 - 13-03-2024
 
 Initial release of qbic-pipelines/vcftomaf, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -58,6 +58,11 @@ nextflow run qbic-pipelines/vcftomaf \
 > 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).
 
+For more details and further functionality, please refer to the [usage documentation](docs/usage.md) and the [parameter documentation](nextflow_schema.json).
+
+For more details about the output files and reports, please refer to the
+[output documentation](docs/output.md).
+
 ## Credits
 
 qbic-pipelines/vcftomaf was originally written by [SusiJo](https://github.com/SusiJo) and [Friederike Hanssen](https://github.com/FriederikeHanssen)

docs/usage.md

@@ -94,13 +94,13 @@ Chain file, if liftover should be done
 The input vcf files are PASS filtered by default.
 Additionally, if the path to a file containing the targeted intervals for panel sequencing data is specified, off-target regions will be filtered out.
 
-### `--vep_cache`
+<!-- ### `--vep_cache`
 
 Please provide a path to a compressed vep-cache file if you wish to run vep.
 
 ### `--run_vep`
 
-Set to true if you wish to run vep. Default is false.
+Set to true if you wish to run vep. Default is false. -->
 
 ### Params file