Clean up nf-test tests and snapshot (#1809)

Close #1807

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## PR checklist

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add
tests!
- [ ] If you've added a new tool - have you followed the pipeline
conventions in the [contribution
docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/nf-core/test-datasets)
repository.
- [ ] Make sure your code lints (`nf-core pipelines lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker
--outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run .
-profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and
authors/contributors).

CHANGELOG.md

@@ -15,10 +15,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [1806](https://github.com/nf-core/sarek/pull/1806) - Migrate pipeline pytest vcf concatenation tests to nf-test
+- [1809](https://github.com/nf-core/sarek/pull/1809) - Replace `getReadsMD5()` by `readsMD5` from `nft-bam` plugin for more global cohesion with usage of `nft-vcf` plugin
 
 ### Fixed
 
 - [1806](https://github.com/nf-core/sarek/pull/1806) - Fix some nf-test assertions
+- [1809](https://github.com/nf-core/sarek/pull/1809) - Deals with nf-test snapshoting empty lists in a better way (https://github.com/nf-core/sarek/issues/1807)
 
 ### Removed
 

tests/aligner-bwa-mem.nf.test

@@ -38,7 +38,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }

tests/aligner-bwa-mem2.nf.test

@@ -38,7 +38,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }

tests/aligner-dragmap.nf.test

@@ -38,7 +38,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }

tests/default.nf.test

@@ -36,7 +36,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] },
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] },
                     // All vcf files
                     vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5] }
                 ).match() }

tests/save_output_as_bam.nf.test

@@ -33,9 +33,9 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path,
+                    stable_path.isEmpty() ? 'No stable content' : stable_path,
                     // All bam files
-                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).readsMD5 ] }
                 ).match() }
             )
         }

tests/save_output_as_bam.nf.test.snap

@@ -32,9 +32,7 @@
                 "preprocessing/mapped/test/test.sorted.bam.bai",
                 "reference"
             ],
-            [
-
-            ],
+            "No stable content",
             [
                 [
                     "test.sorted.bam",
@@ -43,9 +41,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.09.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:11:44.283548"
+        "timestamp": "2025-02-25T10:18:22.407985941"
     }
-}
+}

tests/saved_mapped.nf.test

@@ -35,9 +35,9 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path,
+                    stable_path.isEmpty() ? 'No stable content' : stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }

tests/saved_mapped.nf.test.snap

@@ -32,9 +32,7 @@
                 "preprocessing/mapped/test/test.sorted.cram.crai",
                 "reference"
             ],
-            [
-
-            ],
+            "No stable content",
             [
                 [
                     "test.sorted.cram",
@@ -46,6 +44,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-24T19:13:29.577785838"
+        "timestamp": "2025-02-25T10:19:32.705278311"
     }
 }

tests/sentieon.nf.test

@@ -40,7 +40,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }

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 {
@@ -37,13 +37,13 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }
     }
 
-    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 {
@@ -76,14 +76,14 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.isEmpty() ? 'No CRAM files' : cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }
     }
 
 
-    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 {
@@ -115,13 +115,13 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }
     }
 
-    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 {
@@ -154,7 +154,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }

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,
             {
@@ -114,17 +114,15 @@
                 "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
                 "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac"
             ],
-            [
-
-            ]
+            "No CRAM files"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-09T16:15:20.865586"
+        "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,
             {
@@ -303,7 +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,
             {
@@ -451,7 +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,
             {
@@ -630,4 +628,4 @@
         },
         "timestamp": "2024-11-09T16:18:25.238396"
     }
-}
+}

tests/start_from_preparerecalibration.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 prepare_recalibration --tools null ") {
+    test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null") {
 
         when {
             params {
@@ -25,8 +25,6 @@ nextflow_pipeline {
             // cram_files: All cram files
             def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
             def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
-            // vcf_files: All vcf files
-            def vcf_files  = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -39,15 +37,13 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] },
-                    // All vcf files
-                    vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5] }
+                    cram_files.isEmpty() ? 'No CRAM files' : cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }
     }
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ") {
+    test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka") {
 
         when {
             params {
@@ -82,7 +78,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] },
+                    cram_files.isEmpty() ? 'No CRAM files' : cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] },
                     // All vcf files
                     vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5] }
                 ).match() }
@@ -91,7 +87,7 @@ nextflow_pipeline {
     }
 
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null ") {
+    test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null") {
 
         when {
             params {
@@ -111,8 +107,6 @@ nextflow_pipeline {
             // cram_files: All cram files
             def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
             def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
-            // vcf_files: All vcf files
-            def vcf_files  = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -125,15 +119,13 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] },
-                    // All vcf files
-                    vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5] }
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] }
                 ).match() }
             )
         }
     }
 
-    test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ") {
+    test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka") {
 
         when {
             params {
@@ -168,7 +160,7 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // All cram files
-                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] },
+                    cram_files.isEmpty() ? 'No CRAM files' : cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).readsMD5 ] },
                     // All vcf files
                     vcf_files.collect{ file -> [ file.getName(), path(file.toString()).vcf.variantsMD5] }
                 ).match() }