Added nf-test for atlas/pmd (#6346)

* Added nf-test for atlas/pmd

* Fixed power assertion

---------

Co-authored-by: Simon Pearce <[email protected]>

modules/nf-core/atlas/pmd/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

modules/nf-core/atlas/pmd/tests/main.nf.test

@@ -0,0 +1,46 @@
+
+nextflow_process {
+
+    name "Test Process ATLAS_PMD"
+    script "../main.nf"
+    process "ATLAS_PMD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "atlas"
+    tag "atlas/pmd"
+
+    test("test-atlas-pmd") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+				    []
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.empiric[0][1]).readLines()[0],
+					file(process.out.exponential[0][1]).readLines()[0][0..13],
+					file(process.out.counts[0][1]).readLines()[0],
+					file(process.out.table[0][1]).readLines()[0],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/atlas/pmd/tests/main.nf.test.snap

@@ -0,0 +1,18 @@
+{
+    "test-atlas-pmd": {
+        "content": [
+            "1\tCT\tEmpiric[0.000831,0.000000,0.001339,0.001350,0.001437,0.000000,0.002210,0.001314,0.001466,0.000000,0.001395,0.001403,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.001362,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000794,0.000000,0.000000,0.000000,0.001297,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000]",
+            "1\tExponential[",
+            "1\tforward\tA->A\t2050\t2033\t2081\t2078\t2138\t2119\t2038\t2007\t2035\t2113\t2049\t2048\t1974\t2012\t2066\t2093\t2110\t1971\t1976\t1906\t1968\t1951\t1917\t1912\t1955\t1956\t1933\t1872\t1922\t1933\t1974\t1840\t1963\t1897\t1870\t1823\t1923\t1908\t1902\t1883\t1973\t1899\t1908\t1912\t1972\t1913\t1922\t1959\t1995\t2039",
+            "1\tforward\tA->A\t0.998539\t0.997547\t0.997603\t1\t0.998133\t0.998586\t0.99902\t0.998507\t0.998038\t0.999527\t0.997566\t0.997565\t0.998988\t0.998016\t0.99855\t0.999522\t0.996223\t0.99848\t0.999494\t0.998952\t0.999492\t0.997444\t0.998958\t0.997912\t0.997958\t0.997959\t0.997935\t0.998933\t0.996888\t0.999483\t0.998988\t0.999457\t0.998474\t0.998947\t0.998398\t0.998357\t0.997924\t0.999476\t0.999475\t1\t0.998987\t0.998423\t0.999476\t1\t1\t0.998956\t0.998442\t0.997454\t0.9975\t0.99951",
+            [
+                "versions.yml:md5,abec49256c52cb677fa0dad3473ed5a6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T16:01:09.837624"
+    }
+}

tests/config/pytest_modules.yml

@@ -25,9 +25,6 @@ ataqv/ataqv:
 ataqv/mkarv:
   - modules/nf-core/ataqv/mkarv/**
   - tests/modules/nf-core/ataqv/mkarv/**
-atlas/pmd:
-  - modules/nf-core/atlas/pmd/**
-  - tests/modules/nf-core/atlas/pmd/**
 atlas/splitmerge:
   - modules/nf-core/atlas/splitmerge/**
   - tests/modules/nf-core/atlas/splitmerge/**