Switch to nf-bam plugin for output validation.

nf-core · Nov 25, 2024 · ff07ff9 · ff07ff9
1 parent ad3f4e7
commit ff07ff9
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Showing 8 changed files with 37 additions and 67 deletions.
diff --git a/modules/nf-core/umicollapse/tests/main.nf.test b/modules/nf-core/umicollapse/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "umicollapse"
-    tag "umitools/extract"
-    tag "samtools/index"
-    tag "bwa/index"
-    tag "bwa/mem"
 
     test("umicollapse single end test") {
 
@@ -32,7 +28,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    bam(process.out.bam[0][1]).getSamLinesMD5(),
                     process.out.versions).match() }
             )
         }
@@ -59,7 +55,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.bam,
+                    bam(process.out.bam[0][1]).getSamLinesMD5(),
                     process.out.versions).match() }
             )
         }

diff --git a/modules/nf-core/umicollapse/tests/main.nf.test.snap b/modules/nf-core/umicollapse/tests/main.nf.test.snap
@@ -1,15 +1,7 @@
 {
     "umicollapse single end test": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test.dedup.bam:md5,77e83b5d15bb188de1149bf49c4c7b51"
-                ]
-            ],
+            "9158ea6e7a0e54819e25cbac5fbc5cc0",
             [
                 "versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1"
             ]
@@ -18,18 +10,11 @@
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-24T13:57:11.593685"
+        "timestamp": "2024-11-25T17:31:45.024306"
     },
     "umicollapse paired tests": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.dedup.bam:md5,09cfdd25a90ae5bd7c78912984feadbe"
-                ]
-            ],
+            "b7be15ac7aae194b04bdbb56f3534495",
             [
                 "versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1"
             ]
@@ -38,7 +23,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-24T13:57:20.582394"
+        "timestamp": "2024-11-25T17:31:52.072799"
     },
     "umicollapse fastq test (paired-end)": {
         "content": [

diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test
@@ -61,7 +61,7 @@ nextflow_process {
                 { assert process.success },
                 { assert path("${process.out.log[0][1]}").exists() },
                 { assert snapshot(
-                    process.out.bam,
+                    bam(process.out.bam[0][1]).getSamLinesMD5(),
                     process.out.versions).match() }
             )
         }
@@ -90,7 +90,7 @@ nextflow_process {
                 { assert process.success },
                 { assert path("${process.out.log[0][1]}").exists() },
                 { assert snapshot(
-                    process.out.bam,
+                    bam(process.out.bam[0][1]).getSamLinesMD5(),
                     process.out.tsv_edit_distance,
                     process.out.tsv_per_umi,
                     process.out.tsv_umi_per_position,

diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test.snap b/modules/nf-core/umitools/dedup/tests/main.nf.test.snap
@@ -37,15 +37,7 @@
     },
     "pe - with stats": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.dedup.bam:md5,3c44698572f108dd5a9bd205375be2b8"
-                ]
-            ],
+            "b7be15ac7aae194b04bdbb56f3534495",
             [
                 [
                     {
@@ -81,7 +73,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-23T09:08:10.434136"
+        "timestamp": "2024-11-25T17:25:28.939957"
     },
     "se - no stats - stub": {
         "content": [
@@ -116,15 +108,7 @@
     },
     "pe - no stats": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.dedup.bam:md5,3c44698572f108dd5a9bd205375be2b8"
-                ]
-            ],
+            "b7be15ac7aae194b04bdbb56f3534495",
             [
                 "versions.yml:md5,e2f5146464c09bf7ae98c85ea5410e50"
             ]
@@ -133,6 +117,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-23T09:07:32.367542"
+        "timestamp": "2024-11-25T17:24:51.423637"
     }
 }
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test
@@ -41,7 +41,8 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out.bam, workflow.out.versions).match() },
+                { assert snapshot(bam(workflow.out.bam[0][1]).getSamLinesMD5()).match("test_bam_dedup_stats_samtools_umicollapse_bam")},  // separate, because of linting error otherwise
+                { assert snapshot(workflow.out.versions).match("test_bam_dedup_stats_samtools_umicollapse_versions") },
                 { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"},
                 { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"},
                 { assert workflow.out.dedup_stats.get(0).get(1) ==~ ".*_UMICollapse.log"},

diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap
@@ -16,46 +16,38 @@
         },
         "timestamp": "2024-11-24T13:57:02.323104"
     },
-    "test_bam_dedup_stats_samtools_umicollapse_flagstats": {
+    "test_bam_dedup_stats_samtools_umicollapse_versions": {
         "content": [
             [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.flagstat:md5,18d602435a02a4d721b78d1812622159"
-                ]
+                "versions.yml:md5,20605eb79c410c0ed179ba660d82f75b",
+                "versions.yml:md5,23617661d2c899996bee2b05db027e25",
+                "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7",
+                "versions.yml:md5,e02a62a393a833778e16542eeed0d148",
+                "versions.yml:md5,ef00762e264b99ac45713dc0dedf4060"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-24T13:57:02.366866"
+        "timestamp": "2024-11-25T18:39:15.637444"
     },
-    "sarscov2_bam_bai": {
+    "test_bam_dedup_stats_samtools_umicollapse_flagstats": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.dedup.bam:md5,09cfdd25a90ae5bd7c78912984feadbe"
+                    "test.flagstat:md5,18d602435a02a4d721b78d1812622159"
                 ]
-            ],
-            [
-                "versions.yml:md5,20605eb79c410c0ed179ba660d82f75b",
-                "versions.yml:md5,23617661d2c899996bee2b05db027e25",
-                "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7",
-                "versions.yml:md5,e02a62a393a833778e16542eeed0d148",
-                "versions.yml:md5,ef00762e264b99ac45713dc0dedf4060"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-24T13:57:02.27027"
+        "timestamp": "2024-11-24T13:57:02.366866"
     },
     "test_bam_dedup_stats_samtools_umicollapse_idxstats": {
         "content": [
@@ -73,5 +65,15 @@
             "nextflow": "24.10.1"
         },
         "timestamp": "2024-11-24T13:57:02.410712"
+    },
+    "test_bam_dedup_stats_samtools_umicollapse_bam": {
+        "content": [
+            "b7be15ac7aae194b04bdbb56f3534495"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-25T18:39:15.613319"
     }
 }
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test
@@ -41,6 +41,7 @@ nextflow_workflow {
                 { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"},
                 { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"},
                 { assert snapshot(
+                    bam(workflow.out.bam[0][1]).getSamLinesMD5(),
                     workflow.out.stats,
                     workflow.out.flagstat,
                     workflow.out.idxstats,

diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "sarscov2_bam_bai": {
         "content": [
+            "b7be15ac7aae194b04bdbb56f3534495",
             [
                 [
                     {
@@ -37,7 +38,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-23T09:16:50.849764"
+        "timestamp": "2024-11-25T17:23:13.841219"
     },
     "sarscov2_bam_bai - stub": {
         "content": [