Change default test profile Space Ranger profile

Change the default test profile from only running downstream analyses to including Space Ranger (v2) processing. This is a better test of pipeline functionality, as it includes all of the steps that the pipeline could include and not just downstream processing.
nf-core · Jan 5, 2024 · 47f4f7f · 47f4f7f
1 parent 5657ec7
commit 47f4f7f
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Showing 7 changed files with 21 additions and 18 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -12,15 +12,15 @@
 
 params {
     config_profile_name        = 'Test profile'
-    config_profile_description = 'Test pipeline for post-Space Ranger functionality'
+    config_profile_description = 'Test pipeline functionality, including Space Ranger v2'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
     max_memory = '3.GB'
     max_time   = '2.h'
 
     // Input and output
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_downstream.csv'
+    input = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_spaceranger.csv"
     spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv"
     spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/homo_sapiens_chr22_reference.tar.gz"
 

diff --git a/conf/test_spaceranger_v2.config → conf/test_downstream.config b/conf/test_spaceranger_v2.config → conf/test_downstream.config
@@ -5,22 +5,22 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/spatialtranscriptomics -profile test_spaceranger,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/spatialtranscriptomics -profile test_downstream,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Space Ranger v2 test profile'
-    config_profile_description = 'Test all pipeline functionality, including Space Ranger v2'
+        config_profile_name        = 'Downstream test profile'
+        config_profile_description = 'Test pipeline for downstream (post-Space Ranger) functionality'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
     max_memory = '3.GB'
     max_time   = '2.h'
 
     // Input and output
-    input = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_spaceranger.csv"
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_downstream.csv'
     spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv"
     spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/homo_sapiens_chr22_reference.tar.gz"
 

diff --git a/conf/test_spaceranger_v1.config b/conf/test_spaceranger_v1.config
@@ -5,14 +5,14 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/spatialtranscriptomics -profile test_spaceranger,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/spatialtranscriptomics -profile test_spaceranger_v1,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
     config_profile_name        = 'Space Ranger v1 test profile'
-    config_profile_description = 'Test all pipeline functionality, including Space Ranger v1'
+    config_profile_description = 'Test pipeline functionality, including Space Ranger v1'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2

diff --git a/nextflow.config b/nextflow.config
@@ -179,9 +179,9 @@ profiles {
         executor.memory        = 8.GB
     }
     test                { includeConfig 'conf/test.config'      }
-    test_full           { includeConfig 'conf/test_full.config' }
     test_spaceranger_v1 { includeConfig 'conf/test_spaceranger_v1.config' }
-    test_spaceranger_v2 { includeConfig 'conf/test_spaceranger_v2.config' }
+    test_downstream     { includeConfig 'conf/test_downstream.config' }
+    test_full           { includeConfig 'conf/test_full.config' }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

diff --git a/tests/pipeline/test_downstream.nf.test b/tests/pipeline/test_downstream.nf.test
@@ -6,7 +6,14 @@ nextflow_pipeline {
     test("Downstream FFPE v2 CytAssist") {
         when {
             params {
-                // This is the default `test` profile; params are not necessary
+                // Input and output
+                input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_downstream.csv'
+                spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv"
+                spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/homo_sapiens_chr22_reference.tar.gz"
+
+                // Parameters
+                st_preprocess_min_counts = 5
+                st_preprocess_min_genes = 3
                 outdir = "$outputDir"
             }
         }

diff --git a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test
@@ -1,5 +1,5 @@
 nextflow_pipeline {
-    name "Test full workflow (incl. Space Ranger)"
+    name "Test full workflow (incl. Space Ranger v1)"
     script "main.nf"
     tag "pipeline"
 

diff --git a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test
@@ -1,16 +1,12 @@
 nextflow_pipeline {
-    name "Test full workflow (incl. Space Ranger)"
+    name "Test full workflow (incl. Space Ranger v2)"
     script "main.nf"
     tag "pipeline"
 
     test("Space Ranger FFPE v2 CytAssist") {
         when {
             params {
-                input = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_spaceranger.csv"
-                spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv"
-                spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/homo_sapiens_chr22_reference.tar.gz"
-                st_preprocess_min_counts = 5
-                st_preprocess_min_genes = 3
+                // This is the default `test` profile; params are not necessary
                 outdir = "$outputDir"
             }
         }