From e6c7939305c2ef5477b0576a0efcbd63800b8e9d Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 23 Aug 2022 14:37:01 +0200
Subject: [PATCH] Add test_nothing config profile for minimal testing

---
 conf/test_nothing.config | 47 ++++++++++++++++++++++++++++++++++++++++
 nextflow.config          | 11 +++++-----
 2 files changed, 53 insertions(+), 5 deletions(-)
 create mode 100644 conf/test_nothing.config

diff --git a/conf/test_nothing.config b/conf/test_nothing.config
new file mode 100644
index 0000000..e4846a3
--- /dev/null
+++ b/conf/test_nothing.config
@@ -0,0 +1,47 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset without performing any profiling 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
+    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    perform_shortread_qc                  = false
+    perform_longread_qc                   = false
+    perform_shortread_complexityfilter    = false
+    perform_shortread_hostremoval         = false
+    perform_longread_hostremoval          = false
+    perform_runmerging                    = false
+    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                             = false
+    run_kraken2                           = false
+    run_malt                              = false
+    run_metaphlan3                        = false
+    run_centrifuge                        = false
+    run_diamond                           = false
+    run_motus                             = false
+}
+
+process {
+    withName: MALT_RUN {
+        maxForks = 1
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index 58c9254..4a83031 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -204,11 +204,12 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
     }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
-    test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
-    test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
-    test_motus { includeConfig 'conf/test_motus.config' }
+    test                    { includeConfig 'conf/test.config'      }
+    test_full               { includeConfig 'conf/test_full.config' }
+    test_noprofiling        { includeConfig 'conf/test_noprofiling.config' }
+    test_nopreprocessing    { includeConfig 'conf/test_nopreprocessing.config' }
+    test_nothing            { includeConfig 'conf/test_nothing.config' }
+    test_motus              { includeConfig 'conf/test_motus.config' }
 }
 
 // Load igenomes.config if required