Porting pipeline to DSL2

[SusiJo]

Many thanks to contributing to qbic-pipelines/bamtofastq!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

• [x] This comment contains a description of changes (with reason)
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If necessary, add test data to testdata/
• [x] Ensure the test suite passes (nextflow run . -profile test,docker).
• [x] Make sure your code lints (nf-core lint .).
• [x] Documentation in docs is updated
• [x] CHANGELOG.md is updated
• [x] README.md is updated

Learn more about contributing: https://github.com/qbic-pipelines/bamtofastq/tree/master/.github/CONTRIBUTING.md

[SusiJo]

Hi @FriederikeHanssen, This is still a Draft PR so no need for a review yet. Since I had some branch issues on the other PR, I decided to make a fresh and cleaner PR. Also we decided to try integrating the pipeline into nf-core, therefore the labels have changed 😉

[FriederikeHanssen]

it would probably be good if we start merging PRs soon-ish to the dsl2, so we can fix things independently. Otherwise, I will have to push to your branch which will cause chaos :D

[SusiJo]

Linting is passing locally with nf-core tools 2.8.dev0. Might be failing because of a missing == in the pipeline template in the master branch that was added on the dev already. See here.