Update issue templates

[ewels]

It seems that the GitHub issue templates have stopped working. This is on all nf-core repos, so I guess it's due to a change in how GitHub handles them.

I used the automated builder feature described in https://docs.github.com/en/free-pro-team@latest/github/building-a-strong-community/configuring-issue-templates-for-your-repository on this repo to make this pull request, mostly to see what it would do. It looks like we just need some additional YAML front-matter at the top of the markdown files.

Hopefully merging this PR will solve the issue. It may be problematic that the PR is to dev and not master, so I'll also try it on one of the core repos where we work on master.

[github-actions[bot]]

Hi @ewels,

It looks like this pull-request is has been made against the nf-core/hic master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the nf-core/hic dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.

Thanks again for your contribution!

[github-actions[bot]]

nf-core lint overall result: Passed :white_check_mark:

Updated for pipeline commit 053c1e9

+| ✅ 102 tests passed       |+
!| ❗ 16 tests had warnings |!
-| ❌  0 tests failed       |-

### :heavy_exclamation_mark: Test warnings: * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::python=3.7.6`, `3.9.0` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `pip=20.0.1`, `20.2.4` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::scipy=1.4.1`, `1.5.3` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::numpy=1.18.1`, `1.19.4` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::bx-python=0.8.8`, `0.8.9` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::pysam=0.15.4`, `0.16.0.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::pymdown-extensions=7.1`, `8.0.1` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::cooler=0.8.6`, `0.8.10` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::bowtie2=2.3.5`, `2.4.2` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::samtools=1.9`, `1.11` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::multiqc=1.8`, `1.9` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::hicexplorer=3.4.3`, `3.5.3` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::bioconductor-hitc=1.32.0`, `1.34.0` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `bioconda::ucsc-bedgraphtobigwig=357`, `377` available * [Test #8](https://nf-co.re/errors#8) - Conda package is not latest available: `conda-forge::cython=0.29.19`, `0.29.21` available * [Test #8](https://nf-co.re/errors#8) - PyPi package is not latest available: 0.8.30, 0.9.7 available ### :white_check_mark: Tests passed: * [Test #1](https://nf-co.re/errors#1) - File found: `nextflow.config` * [Test #1](https://nf-co.re/errors#1) - File found: `nextflow_schema.json` * [Test #1](https://nf-co.re/errors#1) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [Test #1](https://nf-co.re/errors#1) - File found: `README.md` * [Test #1](https://nf-co.re/errors#1) - File found: `CHANGELOG.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/README.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/output.md` * [Test #1](https://nf-co.re/errors#1) - File found: `docs/usage.md` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/branch.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/ci.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/linting.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `main.nf` * [Test #1](https://nf-co.re/errors#1) - File found: `environment.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `Dockerfile` * [Test #1](https://nf-co.re/errors#1) - File found: `conf/base.config` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/awstest.yml` * [Test #1](https://nf-co.re/errors#1) - File found: `.github/workflows/awsfulltest.yml` * [Test #1](https://nf-co.re/errors#1) - File not found check: `Singularity` * [Test #1](https://nf-co.re/errors#1) - File not found check: `parameters.settings.json` * [Test #1](https://nf-co.re/errors#1) - File not found check: `bin/markdown_to_html.r` * [Test #1](https://nf-co.re/errors#1) - File not found check: `.travis.yml` * [Test #3](https://nf-co.re/errors#3) - Licence check passed * [Test #2](https://nf-co.re/errors#2) - Dockerfile check passed * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.name` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.nextflowVersion` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.description` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.version` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.homePage` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `timeline.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `trace.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `report.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `dag.enabled` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.cpus` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.memory` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.time` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `params.outdir` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `params.input` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `manifest.mainScript` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `timeline.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `trace.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `report.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `dag.file` * [Test #4](https://nf-co.re/errors#4) - Config variable found: `process.container` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.version` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.nf_required_version` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.container` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.singleEnd` * [Test #4](https://nf-co.re/errors#4) - Config variable (correctly) not found: `params.igenomesIgnore` * [Test #4](https://nf-co.re/errors#4) - Config `timeline.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `report.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `trace.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `dag.enabled` had correct value: `true` * [Test #4](https://nf-co.re/errors#4) - Config `manifest.name` began with `nf-core/` * [Test #4](https://nf-co.re/errors#4) - Config variable `manifest.homePage` began with https://github.com/nf-core/ * [Test #4](https://nf-co.re/errors#4) - Config `dag.file` ended with `.svg` * [Test #4](https://nf-co.re/errors#4) - Config variable `manifest.nextflowVersion` started with >= or !>= * [Test #4](https://nf-co.re/errors#4) - Config `process.container` looks correct: `nfcore/hic:dev` * [Test #4](https://nf-co.re/errors#4) - Config `manifest.version` ends in `dev`: `'1.3.0dev'` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions 'branch' workflow is triggered for PRs to master: `/home/runner/work/hic/hic/.github/workflows/branch.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions 'branch' workflow looks good: `/home/runner/work/hic/hic/.github/workflows/branch.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions CI is triggered on expected events: `/home/runner/work/hic/hic/.github/workflows/ci.yml` * [Test #5](https://nf-co.re/errors#5) - CI is building the correct docker image: `docker build --no-cache . -t nfcore/hic:dev` * [Test #5](https://nf-co.re/errors#5) - CI is pulling the correct docker image: docker pull nfcore/hic:dev * [Test #5](https://nf-co.re/errors#5) - CI is tagging docker image correctly: docker tag nfcore/hic:dev nfcore/hic:dev * [Test #5](https://nf-co.re/errors#5) - Continuous integration checks minimum NF version: `/home/runner/work/hic/hic/.github/workflows/ci.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions linting workflow is triggered on PR and push: `/home/runner/work/hic/hic/.github/workflows/linting.yml` * [Test #5](https://nf-co.re/errors#5) - Continuous integration runs Markdown lint Tests: `/home/runner/work/hic/hic/.github/workflows/linting.yml` * [Test #5](https://nf-co.re/errors#5) - Continuous integration runs nf-core lint Tests: `/home/runner/work/hic/hic/.github/workflows/linting.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions AWS test is triggered on workflow_dispatch: `/home/runner/work/hic/hic/.github/workflows/awstest.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions AWS full test is triggered only on published release and workflow_dispatch: `/home/runner/work/hic/hic/.github/workflows/awsfulltest.yml` * [Test #5](https://nf-co.re/errors#5) - GitHub Actions AWS full test should test full datasets: `/home/runner/work/hic/hic/.github/workflows/awsfulltest.yml` * [Test #6](https://nf-co.re/errors#6) - README Nextflow minimum version badge matched config. Badge: `19.10.0`, Config: `19.10.0` * [Test #6](https://nf-co.re/errors#6) - README had a bioconda badge * [Test #8](https://nf-co.re/errors#8) - Conda environment name was correct (nf-core-hic-1.3.0dev) * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::python=3.7.6` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `pip=20.0.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::scipy=1.4.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::numpy=1.18.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::iced=0.5.6` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `bioconda::iced=0.5.6` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::bx-python=0.8.8` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::pysam=0.15.4` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::pymdown-extensions=7.1` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::cooler=0.8.6` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::bowtie2=2.3.5` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::samtools=1.9` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::multiqc=1.8` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::hicexplorer=3.4.3` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::bioconductor-hitc=1.32.0` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::r-optparse=1.6.6` * [Test #8](https://nf-co.re/errors#8) - Conda package is latest available: `conda-forge::r-optparse=1.6.6` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `bioconda::ucsc-bedgraphtobigwig=357` * [Test #8](https://nf-co.re/errors#8) - Conda dependency had pinned version number: `conda-forge::cython=0.29.19` * [Test #8](https://nf-co.re/errors#8) - Pip dependency had pinned version number: cooltools==0.3.2 * [Test #8](https://nf-co.re/errors#8) - PyPi package is latest available: 0.3.2 * [Test #8](https://nf-co.re/errors#8) - Pip dependency had pinned version number: fanc==0.8.30 * [Test #9](https://nf-co.re/errors#9) - Found all expected strings in Dockerfile file * [Test #12](https://nf-co.re/errors#12) - Name adheres to nf-core convention * [Test #13](https://nf-co.re/errors#13) - Did not find any cookiecutter template strings (53 files) * [Test #14](https://nf-co.re/errors#14) - Schema lint passed * [Test #14](https://nf-co.re/errors#14) - Schema title + description lint passed * [Test #15](https://nf-co.re/errors#15) - Schema matched params returned from nextflow config ### Run details: * nf-core/tools version 1.11 * Run at `2020-11-07 19:21:41`

[ewels]

Thanks to @RxLoutre for reporting this issue! 🙌🏻

[ewels]

Lint tests failing because the pipeline needs to be updated to the latest version of the template (see https://github.com/nf-core/hic/pull/77) and also because the dev branch has a stable release tag - only master should have this.