Add/fix more stubs (#5563)

* fix some stubs * add more stubs! * fix expansionhunter tests * fix concat tests * Update modules/nf-core/bcftools/sort/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * fix bcftools tests again * fix expansionhunter versions * fix concat again * fix bgzip version for expansionhunter * fix bgzip version for expansionhunter --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
nf-core · May 3, 2024 · b42fec6 · b42fec6
1 parent cdcdd5e
commit b42fec6
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Showing 15 changed files with 429 additions and 67 deletions.
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
@@ -36,7 +36,7 @@ process BCFTOOLS_CONCAT {
     stub:
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test
@@ -34,10 +34,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.vcf,
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -63,10 +60,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.vcf,
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -96,10 +90,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.vcf[0][1]).name,
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 

diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
@@ -1,43 +1,101 @@
 {
     "sarscov2 - [[vcf1, vcf2], []]": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test3"
-                    },
-                    "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test3"
+                        },
+                        "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test3"
+                        },
+                        "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
                 ]
-            ],
-            [
-                "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
-            ]
+            }
         ],
-        "timestamp": "2023-11-29T13:52:27.03724666"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-03T13:22:49.766749302"
     },
     "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test3"
-                    },
-                    "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test3"
+                        },
+                        "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test3"
+                        },
+                        "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
                 ]
-            ],
-            [
-                "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
-            ]
+            }
         ],
-        "timestamp": "2023-11-29T13:52:21.468988293"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-03T13:22:41.119912312"
     },
     "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
         "content": [
-            "test3.vcf.gz",
-            [
-                "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test3"
+                        },
+                        "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test3"
+                        },
+                        "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09"
+                ]
+            }
         ],
-        "timestamp": "2023-11-29T13:41:04.716017811"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-03T13:22:59.90466392"
     }
 }
diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
@@ -49,9 +49,9 @@ process BCFTOOLS_SORT {
                     args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                     args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                     "vcf"
-
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${extension}
+    ${create_cmd} ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test
@@ -9,7 +9,29 @@ nextflow_process {
     tag "bcftools"
     tag "bcftools/sort"
 
-    test("SarsCov2 VCF") {
+    test("sarscov2 - vcf") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("vcf") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - vcf - stub") {
+        options "-stub"
         when {
             process {
                 """

diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "SarsCov2 VCF": {
+    "vcf": {
         "content": [
             {
                 "0": [
@@ -28,8 +28,41 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.04.2"
+            "nextflow": "24.03.0"
         },
-        "timestamp": "2024-03-18T12:50:10.340362246"
+        "timestamp": "2024-05-02T16:55:21.237927554"
+    },
+    "sarscov2 - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.03.0"
+        },
+        "timestamp": "2024-05-03T12:32:50.506309198"
     }
 }
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
@@ -57,9 +57,9 @@ process ENSEMBLVEP_VEP {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
-    touch ${prefix}.tab.gz
-    touch ${prefix}.json.gz
+    echo "" | gzip > ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.tab.gz
+    echo "" | gzip > ${prefix}.json.gz
     touch ${prefix}.summary.html
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/expansionhunter/environment.yml b/modules/nf-core/expansionhunter/environment.yml
@@ -1,7 +1,10 @@
 name: expansionhunter
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
   - bioconda::expansionhunter=5.0.0
+  - bioconda::htslib=1.18
diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf
@@ -40,21 +40,21 @@ process EXPANSIONHUNTER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
+        expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | head -1 | sed 's/^.*ExpansionHunter v//')
         bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//')
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
-    touch ${prefix}.json.gz
+    echo "" | gzip > ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.json.gz
     touch ${prefix}_realigned.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
+        expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | head -1 | sed 's/^.*ExpansionHunter v//')
         bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//')
     END_VERSIONS
     """

diff --git a/modules/nf-core/expansionhunter/tests/main.nf.test b/modules/nf-core/expansionhunter/tests/main.nf.test
@@ -7,7 +7,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "expansionhunter"
 
-    test("expansionhunter") {
+    test("homo_sapiens - [bam,bai], fasta, fai, cat") {
 
         when {
             process {
@@ -25,10 +25,35 @@ nextflow_process {
 
         then {
             assertAll(
-            {assert process.success},
-            {assert path(process.out.vcf.get(0).get(1)).linesGzip.size() == 8},
-            {assert path(process.out.json.get(0).get(1)).linesGzip.size() == 27},
-            {assert snapshot(process.out.bam).match()}
+                {assert process.success},
+                {assert snapshot(process.out).match("expansionhunter")}
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [bam,bai], fasta, fai, cat - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                        ]
+                input[1] = [[id:'fasta'],file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
+                input[2] = [[id:'fasta_fai'],file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]
+                input[3] = [[id:'catalogue'],file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out).match("stub")}
             )
         }