Added nf-test for picard/cleansam (#6297)

Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 26, 2024 · adf8be4 · adf8be4
1 parent e989cd7
commit adf8be4
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Showing 7 changed files with 57 additions and 41 deletions.
diff --git a/modules/nf-core/picard/cleansam/meta.yml b/modules/nf-core/picard/cleansam/meta.yml
@@ -21,7 +21,7 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - sam:
+  - bam:
       type: file
       description: BAM file
       pattern: "*.{bam}"
@@ -35,7 +35,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - sam:
+  - bam:
       type: file
       description: Cleaned BAM file
       pattern: "*.{bam}"

diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test b/modules/nf-core/picard/cleansam/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_CLEANSAM"
+    script "../main.nf"
+    process "PICARD_CLEANSAM"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/cleansam"
+
+    test("test-picard-cleansam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:true ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "test-picard-cleansam": {
+        "content": [
+            "798439cbd7fd81cbcc5078022dc5479d",
+            [
+                "versions.yml:md5,f99b648dc3d150a0561094e3a142ee22"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:36:05.525364"
+    }
+}
diff --git a/...s/nf-core/picard/cleansam/nextflow.config → ...ore/picard/cleansam/tests/nextflow.config b/...s/nf-core/picard/cleansam/nextflow.config → ...ore/picard/cleansam/tests/nextflow.config
@@ -1,7 +1,4 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
         withName: 'PICARD_CLEANSAM'{
             ext.prefix = { "${meta.id}.cleaned"}
         }

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -926,9 +926,6 @@ peka:
 phyloflash:
   - modules/nf-core/phyloflash/**
   - tests/modules/nf-core/phyloflash/**
-picard/cleansam:
-  - modules/nf-core/picard/cleansam/**
-  - tests/modules/nf-core/picard/cleansam/**
 picard/collectinsertsizemetrics:
   - modules/nf-core/picard/collectinsertsizemetrics/**
   - tests/modules/nf-core/picard/collectinsertsizemetrics/**

diff --git a/tests/modules/nf-core/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf
diff --git a/tests/modules/nf-core/picard/cleansam/test.yml b/tests/modules/nf-core/picard/cleansam/test.yml