Added nf-test for untarfiles (#6412)

* Added nf-test for untarfiles * Matched conda versions with docker/singularity using wave containers * Changed test name * Added deprecation message
nf-core · Sep 17, 2024 · 958e4a6 · 958e4a6
1 parent 94ae259
commit 958e4a6
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Showing 8 changed files with 471 additions and 74 deletions.
diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml
@@ -4,5 +4,5 @@ channels:
 
 dependencies:
   - bioconda::grep=3.4
-  - conda-forge::sed=4.7
+  - conda-forge::sed=4.8
   - conda-forge::tar=1.34
diff --git a/modules/nf-core/untarfiles/main.nf b/modules/nf-core/untarfiles/main.nf
@@ -1,11 +1,17 @@
+def deprecation_message = """
+WARNING: This module has been deprecated.
+
+Reason:
+This module is no longer recommended for use. It is recommended to use nf-core/modules/untar
+"""
 process UNTARFILES {
     tag "$archive"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+        'oras://community.wave.seqera.io/library/grep_sed_tar:40b34489f8e82876' :
+        'community.wave.seqera.io/library/grep_sed_tar:16f6591cd62505b3' }"
 
     input:
     tuple val(meta), path(archive)
@@ -18,6 +24,7 @@ process UNTARFILES {
     task.ext.when == null || task.ext.when
 
     script:
+    assert true: deprecation_message
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
@@ -39,6 +46,7 @@ process UNTARFILES {
     """
 
     stub:
+    assert true: deprecation_message
     prefix    = task.ext.prefix ?: "${meta.id}"
     """
     mkdir $prefix

diff --git a/modules/nf-core/untarfiles/tests/main.nf.test b/modules/nf-core/untarfiles/tests/main.nf.test
@@ -0,0 +1,104 @@
+
+nextflow_process {
+
+    name "Test Process UNTARFILES"
+    script "../main.nf"
+    process "UNTARFILES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untarfiles"
+
+    test("test-untarfiles") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-untarfiles-subdirectories") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.files[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-untarfiles-onlyfiles") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-untarfiles-onlyfiles-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}