Merge pull request #482 from nf-core/dev

Version 1.8 release

Author: drpatelh

.github/CONTRIBUTING.md

@@ -38,7 +38,7 @@ The HTML will then be generated in `docs/api/_build/html`.
 
 
 ## Tests
-When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic tests.
+When you create a pull request with changes, [Travis CI](https://travis-ci.com/) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
 There are two types of tests that run:

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,4 +1,4 @@
-Many thanks to contributing to nf-core/tools!
+Many thanks for contributing to nf-core/tools!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
 

.github/markdownlint.yml

@@ -1,10 +1,7 @@
 # Markdownlint configuration file
 default: true,
 line-length: false
-no-multiple-blanks: 0
-blanks-around-headers: false
-blanks-around-lists: false
-header-increment: false
 no-duplicate-header:
     siblings_only: true
 no-bare-urls: false # tools only - the {{ jinja variables }} break URLs and cause this to error
+commands-show-output: false # tools only - suppresses error messages for usage of $ in main README

.travis.yml

@@ -2,7 +2,6 @@ sudo: required
 language: python
 jdk: openjdk8
 python:
-  - '2.7'
   - '3.5'
   - '3.6'
   - '3.7'
@@ -42,7 +41,7 @@ jobs:
   include:
     - stage: docs generation
       if: (branch = "master" OR branch = "dev") AND type = push AND repo = nf-core/tools
-      script: bash ./bin/push.sh
+      script: bash ./bin/build_api_docs.sh
 
 deploy:
   provider: pypi
@@ -57,4 +56,4 @@ deploy:
 
 # Sync pipelines with possible nf-core template changes
 after_deploy:
-  - ./bin/sync
+  - nf-core sync --all

CHANGELOG.md

@@ -1,10 +1,77 @@
 # nf-core/tools: Changelog
 
-## v1.7
+## v1.8
 
-### PyPI package description
+### Continuous integration
 
-* The readme should now be rendered properly on PyPI.
+* GitHub Actions CI workflows are now included in the template pipeline
+  * Please update these files to match the existing tests that you have in `.travis.yml`
+* Travis CI tests will be deprecated from the next `tools` release
+* Linting will generate a warning if GitHub Actions workflows do not exist and if applicable to remove Travis CI workflow file i.e. `.travis.yml`.
+
+### Tools helper code
+
+* Refactored the template synchronisation code to be part of the main nf-core tool
+* `nf-core bump-version` now also bumps the version string of the exported conda environment in the Dockerfile
+* Updated Blacklist of synced pipelines
+* Ignore pre-releases in `nf-core list`
+* Updated documentation for `nf-core download`
+* Fixed typo in `nf-core launch` final command
+* Handle missing pipeline descriptions in `nf-core list`
+
+### Linting
+
+* Adjusted linting to enable `patch` branches from being tested
+* Warn if GitHub Actions workflows do not exist, warn if `.travis.yml` and circleCI are there
+* Lint for `Singularity` file and raise error if found [#458](https://github.com/nf-core/tools/issues/458)
+* Added linting of GitHub Actions workflows `linting.yml`, `ci.yml` and `branch.yml`
+* Warn if pipeline name contains upper case letters or non alphabetical characters [#85](https://github.com/nf-core/tools/issues/85)
+* Make CI tests of lint code pass for releases
+
+### Template pipeline
+
+* Fixed incorrect paths in iGenomes config as described in issue [#418](https://github.com/nf-core/tools/issues/418)
+* Fixed incorrect usage of non-existent parameter in the template [#446](https://github.com/nf-core/tools/issues/446)
+* Add UCSC genomes to `igenomes.config` and add paths to all genome indices
+* Change `maxMultiqcEmailFileSize` parameter to `max_multiqc_email_size`
+* Export conda environment in Docker file [#349](https://github.com/nf-core/tools/issues/349)
+* Change remaining parameters from `camelCase` to `snake_case` [#39](https://github.com/nf-core/hic/issues/39)
+  * `--singleEnd` to `--single_end`
+  * `--igenomesIgnore` to `--igenomes_ignore`
+  * Having the old camelCase versions of these will now throw an error
+* Add `autoMounts=true` to default singularity profile
+* Add in `markdownlint` checks that were being ignored by default
+* Disable ansi logging in the travis CI tests
+* Move `params`section from `base.config` to `nextflow.config`
+* Use `env` scope to export `PYTHONNOUSERSITE` in `nextflow.config` to prevent conflicts with host Python environment
+* Bump minimum Nextflow version to `19.10.0` - required to properly use `env` scope in `nextflow.config`
+* Added support for nf-tower in the travis tests, using public mailbox [email protected]
+* Add link to [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and [Semantic Versioning](http://semver.org/spec/v2.0.0.html) to CHANGELOG
+* Adjusted `.travis.yml` checks to allow for `patch` branches to be tested
+* Add Python 3.7 dependency to the `environment.yml` file
+* Remove `awsbatch` profile cf [nf-core/configs#71](https://github.com/nf-core/configs/pull/71)
+* Make `scrape_software_versions.py` compatible with Python3 to enable miniconda3 in    [base image PR](https://github.com/nf-core/tools/pull/462)
+* Add GitHub Actions workflows and respective linting
+* Add `NXF_ANSI_LOG` as global environment variable to template GitHub Actions CI workflow
+* Fixed global environment variable in GitHub Actions CI workflow
+* Add `--awscli` parameter
+* Add `README.txt` path for genomes in `igenomes.config` [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75)
+* Fix buggy ANSI codes in pipeline summary log messages
+* Add a `TODO` line in the new GitHub Actions CI test files
+
+### Base Docker image
+
+* Use miniconda3 instead of miniconda for a Python 3k base environment
+  * If you still need Python 2 for your pipeline, add `conda-forge::python=2.7.4` to the dependencies in your `environment.yml`
+* Update conda version to 4.7.12
+
+### Other
+
+* Updated Base Dockerfile to Conda 4.7.10
+* Entirely switched from Travis-Ci.org to Travis-Ci.com for template and tools
+* Improved core documentation (`-profile`)
+
+## v1.7
 
 ### Tools helper code
 
@@ -17,6 +84,7 @@
 * When listing pipelines, a nicer message is given for the rare case of a detached `HEAD` ref in a locally pulled pipeline. [#297](https://github.com/nf-core/tools/issues/297)
 * The `download` command can now compress files into a single archive.
 * `nf-core create` now fetches a logo for the pipeline from the nf-core website
+* The readme should now be rendered properly on PyPI.
 
 ### Syncing
 
@@ -29,7 +97,7 @@
 
 * If the container slug does not contain the nf-core organisation (for example during development on a fork), linting will raise a warning, and an error with release mode on
 
-### Template
+### Template pipeline
 
 * Add new code for Travis CI to allow PRs from patch branches too
 * Fix small typo in central readme of tools for future releases
@@ -46,6 +114,7 @@
   an AWS S3 bucket as the `--outdir`.
 * Fix workflow.onComplete() message when finishing pipeline
 * Update URL for joining the nf-core slack to https://nf-co.re/join/slack
+* Add GitHub Action for CI and Linting
 * [Increased default time limit](https://github.com/nf-core/tools/issues/370) to 4h
 * Add direct link to the pipeline slack channel in the contribution guidelines
 * Add contributions and support heading with links to contribution guidelines and link to the pipeline slack channel in the main README
@@ -217,7 +286,7 @@ Very large release containing lots of work from the first nf-core hackathon, hel
   * New pipelines are now created using the command `nf-core create`
   * The nf-core template and associated linting are now controlled under the same version system
 * Large number of template updates and associated linting changes
-  * New simplified cookicutter variable usage
+  * New simplified cookiecutter variable usage
   * Refactored documentation - simplified and reduced duplication
   * Better `manifest` variables instead of `params` for pipeline name and version
   * New integrated nextflow version checking

Dockerfile

@@ -1,6 +1,6 @@
-FROM continuumio/miniconda:4.6.14
+FROM continuumio/miniconda3:4.7.12
 LABEL authors="[email protected],[email protected]" \
       description="Docker image containing base requirements for the nfcore pipelines"
 
 # Install procps so that Nextflow can poll CPU usage
-RUN apt-get update && apt-get install -y procps && apt-get clean -y
+RUN apt-get update && apt-get install -y procps && apt-get clean -y