diff --git a/CHANGELOG.md b/CHANGELOG.md index 8bed6e5c90..ba8bf35d6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -36,12 +36,14 @@ ## v1.6 -#### Syncing +### Syncing + * Code refactoring to make the script more readable * No travis build failure anymore on sync errors * More verbose logging -#### Template pipeline +### Template pipeline + * awsbatch `work-dir` checking moved to nextflow itself. Removed unsatisfiable check in main.nf template. * Fixed markdown linting * Tools CI testing now runs markdown lint on compiled template pipeline @@ -49,8 +51,10 @@ * Removed Gitter references in `.github/` directories for `tools/` and pipeline template. * Changed `scrape_software_versions.py` to output `.csv` file * Added `export_plots` parameter to multiqc config +* Corrected some typos as listed [here](https://github.com/nf-core/tools/issues/348) to Guidelines + +### Tools helper code -#### Tools helper code * Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available * Updated main help command to sort the subcommands in a more logical order * Updated readme to describe the new `nf-core launch` command @@ -70,7 +74,8 @@ ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark -#### Template pipeline +### Template pipeline + * Dropped Singularity file * Summary now logs details of the cluster profile used if from [nf-core/configs](https://github.com/nf-core/configs) * Dockerhub is used in favor of Singularity Hub for pulling when using the Singularity profile @@ -84,7 +89,8 @@ * Together with nf-core/configs, helper function now checks hostname and suggests a valid config profile * `awsbatch` executor requires the `tracedir` not to be set to an `s3` bucket. -#### Tools helper code +### Tools helper code + * New `nf-core launch` command to interactively launch nf-core pipelines from command-line * Works with a `parameters.settings.json` file shipped with each pipeline * Discovers additional `params` from the pipeline dynamically @@ -107,12 +113,14 @@ * Now correctly validates version pinning for packages from PyPI * Updates for changes to `process.container` definition -#### Other +### Other + * Bump `conda` to 4.6.7 in base nf-core Dockerfile ## [v1.4](https://github.com/nf-core/tools/releases/tag/1.4) - 2018-12-12 Tantalum Butterfly -#### Template pipeline +### Template pipeline + * Institutional custom config profiles moved to github `nf-core/configs` * These will now be maintained centrally as opposed to being shipped with the pipelines in `conf/` * Load `base.config` by default for all profiles @@ -126,7 +134,8 @@ * Travis: Pull the `dev` tagged docker image for testing * Removed UPPMAX-specific documentation from the template. -#### Tools helper code +### Tools helper code + * Make Travis CI tests fail on pull requests if the `CHANGELOG.md` file hasn't been updated * Minor bugfixing in Python code (eg. removing unused import statements) * Made the web requests caching work on multi-user installations @@ -134,6 +143,7 @@ * Linting: Update for Travis: Pull the `dev` tagged docker image for testing ## [v1.3](https://github.com/nf-core/tools/releases/tag/1.3) - 2018-11-21 + * `nf-core create` command line interface updated * Interactive prompts for required arguments if not given * New flag for workflow author @@ -147,6 +157,7 @@ * Added `pip install --upgrade pip` to `.travis.yml` to update pip in the Travis CI environment ## [v1.2](https://github.com/nf-core/tools/releases/tag/1.2) - 2018-10-01 + * Updated the `nf-core release` command * Now called `nf-core bump-versions` instead * New flag `--nextflow` to change the required nextflow version instead @@ -167,6 +178,7 @@ * New GitHub contributing instructions and pull request template ## [v1.1](https://github.com/nf-core/tools/releases/tag/1.1) - 2018-08-14 + Very large release containing lots of work from the first nf-core hackathon, held in SciLifeLab Stockholm. * The [Cookiecutter template](https://github.com/nf-core/cookiecutter) has been merged into tools diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md index b5fbadfd4d..3202cbe6a3 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md @@ -32,7 +32,7 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t There are typically two types of tests that run: ### Lint Tests -The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to. +The nf-core has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation.