Apply suggestions from code review

README.md

@@ -6,6 +6,7 @@
 </h1>[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3589527)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
+[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.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/)

assets/schema_input.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/mag/main/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/mag/master/assets/schema_input.json",
     "title": "nf-core/mag pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",

nextflow.config

@@ -453,7 +453,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/mag'
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
-    defaultBranch   = 'main'
+    defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
     version         = '3.3.1dev'
     doi             = '10.1093/nargab/lqac007'
@@ -487,7 +487,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/mag/blob/main/CITATIONS.md
+    https://github.com/nf-core/mag/blob/master/CITATIONS.md
 """
     }
     summary {

nextflow_schema.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/mag/main/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/mag/master/nextflow_schema.json",
     "title": "nf-core/mag pipeline parameters",
     "description": "Assembly, binning and annotation of metagenomes",
     "type": "object",