From 6d4be4d7d95346627e9f96a83fc346141731a982 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 22 Mar 2024 09:38:53 +0100
Subject: [PATCH 1/2] Add checkm to CI tests

---
 .github/workflows/ci.yml |  1 +
 conf/test_checkm.config  | 36 ++++++++++++++++++++++++++++++++++++
 nextflow.config          |  1 +
 3 files changed, 38 insertions(+)
 create mode 100644 conf/test_checkm.config

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bff474c0..cb669ffd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -64,6 +64,7 @@ jobs:
             test_virus_identification,
             test_single_end,
             test_concoct,
+            test_checkm,
           ]
     steps:
       - name: Free some space
diff --git a/conf/test_checkm.config b/conf/test_checkm.config
new file mode 100644
index 00000000..904f6bef
--- /dev/null
+++ b/conf/test_checkm.config
@@ -0,0 +1,36 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test CheckM profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input                         = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv'
+    centrifuge_db                 = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
+    kraken2_db                    = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
+    skip_krona                    = false
+    min_length_unbinned_contigs   = 1
+    max_unbinned_contigs          = 2
+    binqc_tool                    = 'checkm'
+    checkm_download_url           = "https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz"
+    checkm_db                     = null
+    save_checkm_data              = false
+    skip_gtdbtk                   = true
+    gtdbtk_min_completeness       = 0
+    skip_concoct                  = true
+}
diff --git a/nextflow.config b/nextflow.config
index 35944b81..dc7fa958 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -318,6 +318,7 @@ profiles {
     test_virus_identification { includeConfig 'conf/test_virus_identification.config' }
     test_single_end           { includeConfig 'conf/test_single_end.config'           }
     test_concoct              { includeConfig 'conf/test_concoct.config'              }
+    test_checkm               { includeConfig 'conf/test_checkm.config'              }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

From 81e0104fa72ca1cd40a40a806c7b5d0afb0f775d Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 22 Mar 2024 09:40:31 +0100
Subject: [PATCH 2/2] Update changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 64fd254c..1fd47121 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#605](https://github.com/nf-core/mag/pull/605) - Added dedicated test profile for CheckM (by @jfy133)
+
 ### `Changed`
 
 ### `Fixed`