Change CI tests

.github/workflows/ci.yml

@@ -51,7 +51,7 @@ jobs:
     strategy:
       matrix:
         # Run remaining test profiles with minimum nextflow version
-        profile: [test_host_rm, test_hybrid, test_hybrid_host_rm]
+        profile: [test_host_rm, test_hybrid, test_hybrid_host_rm, test_busco_auto]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#191](https://github.com/nf-core/mag/pull/191) - Update to nf-core 1.14 `TEMPLATE`
 - [#193](https://github.com/nf-core/mag/pull/193) - Compress CAT output files [#180](https://github.com/nf-core/mag/issues/180)
 - [#198](https://github.com/nf-core/mag/pull/198) - Requires nextflow version `>= 21.04.0`
+- [#200](https://github.com/nf-core/mag/pull/200) - Small changes in GitHub Actions tests
 
 ### `Fixed`
 

conf/test.config

@@ -22,5 +22,6 @@ params {
   skip_krona = true
   min_length_unbinned_contigs = 1
   max_unbinned_contigs = 2
+  busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
   gtdb = false
 }

conf/test_busco_auto.config

@@ -0,0 +1,24 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/mag -profile test_busco_auto,<docker/singularity>
+ */
+
+params {
+  config_profile_name = 'Test 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 = 48.h
+
+  // Input data
+  input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.csv'
+  skip_spades = true
+  min_length_unbinned_contigs = 1
+  max_unbinned_contigs = 2
+  gtdb = false
+}

conf/test_host_rm.config

@@ -18,10 +18,8 @@ params {
   // Input data
   host_fasta = "https://github.com/nf-core/test-datasets/raw/mag/host_reference/genome.hg38.chr21_10000bp_region.fa"
   input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.host_rm.csv'
-  centrifuge_db = "https://github.com/nf-core/test-datasets/raw/mag/test_data/minigut_cf.tar.gz"
-  kraken2_db = "https://github.com/nf-core/test-datasets/raw/mag/test_data/minigut_kraken.tgz"
-  skip_krona = true
   min_length_unbinned_contigs = 1
   max_unbinned_contigs = 2
+  busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
   gtdb = false
 }

conf/test_hybrid.config

@@ -19,5 +19,6 @@ params {
   input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.hybrid.csv'
   min_length_unbinned_contigs = 1
   max_unbinned_contigs = 2
+  busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
   gtdb = false
 }

conf/test_hybrid_host_rm.config

@@ -20,5 +20,6 @@ params {
   input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.hybrid_host_rm.csv'
   min_length_unbinned_contigs = 1
   max_unbinned_contigs = 2
+  busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
   gtdb = false
 }

docs/usage.md

@@ -92,7 +92,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
   * A generic configuration profile to be used with [Conda](https://conda.io/docs/)
   * Pulls most software from [Bioconda](https://bioconda.github.io/)
-* `test`, `test_hybrid`, `test_host_rm`, `test_hybrid_host_rm`
+* `test`, `test_hybrid`, `test_host_rm`, `test_hybrid_host_rm`, `test_busco_auto`
   * Profiles with a complete configuration for automated testing
   * Includes links to test data so needs no other parameters
 

nextflow.config

@@ -190,11 +190,12 @@ profiles {
     podman.enabled           = false
     shifter.enabled          = false
   }
-  test { includeConfig 'conf/test.config' }
-  test_host_rm { includeConfig 'conf/test_host_rm.config' }
-  test_hybrid { includeConfig 'conf/test_hybrid.config' }
+  test                { includeConfig 'conf/test.config'                }
+  test_host_rm        { includeConfig 'conf/test_host_rm.config'        }
+  test_hybrid         { includeConfig 'conf/test_hybrid.config'         }
   test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' }
-  test_full { includeConfig 'conf/test_full.config' }
+  test_busco_auto     { includeConfig 'conf/test_busco_auto.config'     }
+  test_full           { includeConfig 'conf/test_full.config'           }
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container