nf-core/tools: 1.8 - Black Sheep

Continuous integration 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 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 Make CI tests of lint code pass for releases Template pipeline Fixed incorrect paths in iGenomes config as described in issue #418 Fixed incorrect usage of non-existent parameter in the template #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 Change remaining parameters from camelCase to snake_case #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 paramssection 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 nf-core@mailinator.com Add link to Keep a Changelog and Semantic Versioning 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 Make scrape_software_versions.py compatible with Python3 to enable miniconda3 in base image PR 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 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