update readme and ci

Author: tensulin

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,12 +13,6 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/jlab/refbase
 
 ## PR checklist
 
+- [ ] linting passes
 - [ ] This comment contains a description of changes (with reason).
-- [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/jlab/refbasedassemblereval/tree/master/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
-- [ ] Usage Documentation in `docs/usage.md` is updated.
-- [ ] Output Documentation in `docs/output.md` is updated.
-- [ ] `CHANGELOG.md` is updated.
 - [ ] `README.md` is updated (including new tool citations and authors/contributors).

.github/workflows/linting.yml

@@ -1,4 +1,4 @@
-name: nf-core linting
+name: linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.

.github/workflows/linting_comment.yml

@@ -1,10 +1,10 @@
-name: nf-core linting comment
+name: linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
 
 on:
   workflow_run:
-    workflows: ["nf-core linting"]
+    workflows: [linting"]
 
 jobs:
   test:

README.md

@@ -1,9 +1,10 @@
-[![GitHub Actions Linting Status](https://github.com/jlab/refbasedassemblereval/workflows/nf-core%20linting/badge.svg)](https://github.com/jlab/refbasedassemblereval/actions?query=workflow%3A%22nf-core+linting%22)
+[![GitHub Actions Linting Status](https://github.com/jlab/refbasedassemblereval/workflows/linting/badge.svg)](https://github.com/jlab/refbasedassemblereval/actions?query=workflow%3A%22linting%22)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+[![run with apptainer](https://img.shields.io/badge/run%20with-apptainer-1d355c.svg?labelColor=000000)](https://apptainer.org/)
+
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/jlab/refbasedassemblereval)
 
 # ORB (Omics reference based benchmarking)