Merge pull request #3838 from nf-core/dev

Merge pull request #3833 from nf-core/dev

dev > main for 3.4.0 release

fix version number

Merge pull request #3602 from nf-core/dev

Merge pull request #3589 from nf-core/dev

dev > main for 3.3.0 release

Merge pull request #3546 from mirpedrol/patch-3.2.1

merge to main for patch 3.2.1

Merge pull request #3428 from nf-core/dev

dev -> main for 3.2.0 release

Merge pull request #3406 from nf-core/dev

dev -> main for 3.1.2

Merge pull request #3369 from nf-core/dev

dev -> main for 3.1.1

dev -> main for 3.1.0 (#3336)

* set default_branch to master for now

* update changelog

* set git defaultBranch to master in sync action

* update changelog

* use nextflow.config to set defaultBranch

* fix path for nextflow.config grep

* change working dir when setting defaultBranch

* fix Changelog

* Be more verbose in approval check action

* fix if clause

* update changelog

* add verbose mode to sync action

* update changelog

* Apply suggestions from code review

* add input debug for workflow_dispatch sync action

* go back to original directory after configuring git defaultBranch

* add more debugging on sync GHA

* echo message to sync GHA

* try exiting pipeline directory before saving defaultBranch

* cleanup debugging echo

* use same ref in checkout as triggered the workflow

* don't set up loggin level to error

* Revert "don't set up loggin level to error [no changelog]"

* Update nf_core/pipeline-template/.github/workflows/awsfulltest.yml

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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>