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61 changes: 38 additions & 23 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,40 +1,55 @@
# nf-core/tools: Changelog

## 1.14dev
## [v1.14 - Brass Chicken :chicken:](https://github.com/nf-core/tools/releases/tag/1.14) - [2021-05-11]

### Tools
### Template

* Strip values from `nf-core launch` web response which are False and have no default in the schema [[#976](https://github.com/nf-core/tools/issues/976)]
* Try to fix the fix for the automated sync when we submit too many PRs at once [[#970](https://github.com/nf-core/tools/issues/970)]
* Fixed an issue regarding explicit disabling of unused container engines [[#972](https://github.com/nf-core/tools/pull/972)]
* Removed trailing slash from `params.igenomes_base` to yield valid s3 paths (previous paths work with Nextflow but not aws cli)
* Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
* Rewrite the `params_summary_log()` function to properly ignore unset params and have nicer formatting [[#971](https://github.com/nf-core/tools/issues/971)]
* Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
* Convert `d` to `day` in the `cleanParameters` function to make Duration objects like `2d` pass the validation [[#858](https://github.com/nf-core/tools/issues/858)]
* Added nextflow version to quick start section and adjusted `nf-core bump-version` [[#1032](https://github.com/nf-core/tools/issues/1032)]
* Use latest stable Nextflow version `21.04.0` for CI tests instead of the `-edge` release

### Download

* Fix bug in `nf-core download` where image names were getting a hyphen in `nf-core` which was breaking things.
* Extensive new interactive prompts for all command line flags [[#1027](https://github.com/nf-core/tools/issues/1027)]
* It is now recommended to run `nf-core download` without any cli options and follow prompts (though flags can be used to run non-interactively if you wish)
* New helper code to set `$NXF_SINGULARITY_CACHEDIR` and add to `.bashrc` if desired [[#1027](https://github.com/nf-core/tools/issues/1027)]

### Launch

* Strip values from `nf-core launch` web response which are `False` and have no default in the schema [[#976](https://github.com/nf-core/tools/issues/976)]
* Improve API caching code when polling the website, fixes noisy log message when waiting for a response [[#1029](https://github.com/nf-core/tools/issues/1029)]
* New interactive prompts for pipeline name [[#1027](https://github.com/nf-core/tools/issues/1027)]

### Modules

* Added `tool_name_underscore` to the module template to allow TOOL_SUBTOOL in `main.nf` [[#1011](https://github.com/nf-core/tools/issues/1011)]
* Added `--conda-name` flag to `nf-core modules create` command to allow sidestepping questionary [[#988](https://github.com/nf-core/tools/issues/988)]
* Extended `nf-core modules lint` functionality to check tags in `test.yml` and to look for a entry in the `pytest_software.yml` file
* Update `modules` commands to use new test tag format `tool/subtool`
* Rewrite how the tools documentation is deployed to the website, to allow multiple versions
* Created new Docker image for the tools cli package - see installation docs for details [[#917](https://github.com/nf-core/tools/issues/917)]
* New modules lint test comparing the `functions.nf` file to the template version
* Modules installed from alternative sources are put in folders based on the name of the source repository

### Linting

* Fix bug in nf-core lint config skipping for the `nextflow_config` test [[#1019](https://github.com/nf-core/tools/issues/1019)]
* New `-k`/`--key` cli option for `nf-core lint` to allow you to run only named lint tests, for faster local debugging
* Ignore permission errors for setting up requests cache directories to allow starting with an invalid or read-only HOME directory
* Merge markers lint test - ignore binary files, allow config to ignore specific files [[#1040](https://github.com/nf-core/tools/pull/1040)]
* New lint test to check if params in `nextflow config` are mentioned in `main.nf` [[#1038](https://github.com/nf-core/tools/issues/1038)]
* New modules lint test comparing the `functions.nf` file to the template version
* Modules installed from alternative sources are put in folders based on the name of the source repository
* Added temporary fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)]
* Added lint checks for missing parameter description and parameters outside of groups [[#1017](https://github.com/nf-core/tools/issues/1017)]
* Added fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)]
* Use latest stable Nextflow version `21.04.0` for CI tests instead of the `-edge` release
* Fix bug in `nf-core download` where image names were getting a hyphen in `nf-core` which was breaking things.
* Improve API caching code when polling the website, fixes noisy log message when waiting for a response [[#1029](https://github.com/nf-core/tools/issues/1029)]
* Added pipeline schema lint checks for missing parameter description and parameters outside of groups [[#1017](https://github.com/nf-core/tools/issues/1017)]

### Template
### General

* Fixed an issue regarding explicit disabling of unused container engines [[#972](https://github.com/nf-core/tools/pull/972)]
* Removed trailing slash from `params.igenomes_base` to yield valid s3 paths (previous paths work with Nextflow but not aws cli)
* Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
* Rewrite the `params_summary_log()` function to properly ignore unset params and have nicer formatting [[#971](https://github.com/nf-core/tools/issues/971)]
* Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
* Added `tool_name_underscore` to the module template to allow TOOL_SUBTOOL in `main.nf` [[#1011](https://github.com/nf-core/tools/issues/1011)]
* Convert `d` to `day` in the `cleanParameters` function to make Duration objects like `2d` pass the validation [[#858](https://github.com/nf-core/tools/issues/858)]
* Added nextflow version to quick start section and adjusted `nf-core bump-version` [[#1032](https://github.com/nf-core/tools/issues/1032)]
* Try to fix the fix for the automated sync when we submit too many PRs at once [[#970](https://github.com/nf-core/tools/issues/970)]
* Rewrite how the tools documentation is deployed to the website, to allow multiple versions
* Created new Docker image for the tools cli package - see installation docs for details [[#917](https://github.com/nf-core/tools/issues/917)]
* Ignore permission errors for setting up requests cache directories to allow starting with an invalid or read-only `HOME` directory

## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]

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2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

from setuptools import setup, find_packages

version = "1.14dev"
version = "1.14"

with open("README.md") as f:
readme = f.read()
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