Merge pull request #171 from nf-core/hot-fixes

Clean up MultiQC and tests
nf-core · Oct 21, 2024 · af25b3f · af25b3f
2 parents f84692e + a989636
commit af25b3f
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Showing 7 changed files with 67 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,10 +13,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#142](https://github.com/nf-core/nascent/pull/142) - Add STAR aligner
 - [#149](https://github.com/nf-core/nascent/pull/149) - Add Software citations to MultiQC
 
+### Fixed
+
+- [#171](https://github.com/nf-core/nascent/pull/171) - Clean up MultiQC report
+
 ### Changed
 
 - [#137](https://github.com/nf-core/nascent/pull/137) - Use singularity containers for PINTS
 - [#142](https://github.com/nf-core/nascent/pull/142) - Updated CHM13 references
+- [#171](https://github.com/nf-core/nascent/pull/171) - Use assertAll in tests
 
 ### Fixed
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -3,6 +3,29 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/nascent/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
+  fastqc:
+    order: 4004
+  fastp:
+    order: 4003
+  star:
+    order: 3000
+  hisat2:
+    order: 3000
+  samtools:
+    order: 3000
+  featurecounts_biotype:
+    order: 3000
+  picard:
+    order: 3000
+  preseq:
+    order: 3000
+  qualimap:
+    order: 3000
+  rseqc:
+    order: 3000
+  umitools:
+    order: 3000
+  # Summaries
   "nf-core-nascent-methods-description":
     order: -1000
   software_versions:
@@ -20,19 +43,14 @@ run_modules:
   - featureCounts
   - homer
 
-module_order:
-  - fastqc:
-      name: "FastQC (raw)"
-      info: "This section of the report shows FastQC results before adapter trimming."
-      path_filters:
-        - "./fastqc/*.zip"
-
 custom_data:
   grohmm_plot:
     section_name: "groHMM TD Plot"
+    description: "Transcription direction (TD) plot generated by groHMM"
+    plot_type: "image"
 sp:
-  my_custom_content_image:
-    fn: "./grohmm/*.tdplot.jpg"
+  grohmm_plot:
+    fn: "*.tdplot_mqc.jpg"
 ignore_images: false
 
 export_plots: true

diff --git a/modules/local/grohmm/parametertuning/tests/main.nf.test b/modules/local/grohmm/parametertuning/tests/main.nf.test
@@ -28,7 +28,10 @@ nextflow_process {
 
         then {
             // FIXME Broken test
-            assert process.failed
+            assertAll(
+                { assert process.failed },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }

diff --git a/modules/local/grohmm/transcriptcalling/tests/main.nf.test b/modules/local/grohmm/transcriptcalling/tests/main.nf.test
@@ -27,8 +27,10 @@ nextflow_process {
         }
 
         then {
-            // FIXME Broken test
-            assert process.failed
+            assertAll(
+                { assert process.failed },
+                { assert snapshot(process.out).match() }
+            )
         }
 
     }

diff --git a/nf-test.config b/nf-test.config
@@ -3,6 +3,7 @@ config {
     testsDir "."
     workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
     configFile "tests/nextflow.config"
+    profile "test"
     plugins {
         load "[email protected]"
     }

diff --git a/subworkflows/local/grohmm/tests/main.nf.test b/subworkflows/local/grohmm/tests/main.nf.test
@@ -27,8 +27,10 @@ nextflow_workflow {
         }
 
         then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
         }
 
     }
@@ -55,8 +57,10 @@ nextflow_workflow {
         }
 
         then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
         }
 
     }
@@ -84,8 +88,10 @@ nextflow_workflow {
         }
 
         then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
         }
 
     }

diff --git a/workflows/tests/aligner/bwa.nf.test b/workflows/tests/aligner/bwa.nf.test
@@ -71,10 +71,13 @@ nextflow_pipeline {
         }
 
         then {
-            assert workflow.success
-            assert snapshot(
-                workflow.trace.tasks().size(),
-            ).match()
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                ).match()
+                }
+            )
         }
     }
 
@@ -91,10 +94,13 @@ nextflow_pipeline {
         }
 
         then {
-            assert workflow.success
-            assert snapshot(
-                workflow.trace.tasks().size(),
-            ).match()
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                ).match()
+                }
+            )
         }
 
     }