Revert "unzip stub, nf-test, snap"

This reverts commit dec35aa.
nf-core · Mar 20, 2024 · e0d708e · e0d708e
1 parent dec35aa
commit e0d708e
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Showing 7 changed files with 36 additions and 75 deletions.
diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf
@@ -20,6 +20,7 @@ process UNZIP {
     script:
     def args = task.ext.args ?: ''
     if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
+
     prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName)
     """
     7za \\
@@ -33,19 +34,4 @@ process UNZIP {
         7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
     END_VERSIONS
     """
-
-    stub:
-    def args = task.ext.args ?: ''
-    if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
-    prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName)
-    """
-    mkdir "${prefix}"
-    touch "${prefix}"/ncbi.map
-    touch "${prefix}"/ncbi.tre
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
-    END_VERSIONS
-    """
 }
diff --git a/modules/nf-core/unzip/tests/main.nf.test b/modules/nf-core/unzip/tests/main.nf.test
diff --git a/modules/nf-core/unzip/tests/tags.yml b/modules/nf-core/unzip/tests/tags.yml
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -2671,6 +2671,9 @@ universc:
 untarfiles:
   - modules/nf-core/untarfiles/**
   - tests/modules/nf-core/untarfiles/**
+unzip:
+  - modules/nf-core/unzip/**
+  - tests/modules/nf-core/unzip/**
 unzipfiles:
   - modules/nf-core/unzipfiles/**
   - tests/modules/nf-core/unzipfiles/**

diff --git a/tests/modules/nf-core/unzip/main.nf b/tests/modules/nf-core/unzip/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNZIP } from '../../../../modules/nf-core/unzip/main.nf'
+
+workflow test_unzip {
+
+    archive = [
+        [],
+        file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+    ]
+
+    UNZIP ( archive )
+}
+
diff --git a/tests/modules/nf-core/unzip/nextflow.config b/tests/modules/nf-core/unzip/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nf-core/unzip/test.yml b/tests/modules/nf-core/unzip/test.yml
@@ -0,0 +1,11 @@
+- name: unzip test_unzip
+  command: nextflow run ./tests/modules/nf-core/unzip -entry test_unzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/unzip/nextflow.config
+  tags:
+    - unzip
+  files:
+    - path: output/unzip/ncbi_taxmap/
+    - path: output/unzip/ncbi_taxmap/ncbi.map
+      md5sum: de30dbba85f9070612b632e2a5a95952
+    - path: output/unzip/ncbi_taxmap/ncbi.tre
+      md5sum: 4029dd2091c685b9a86ddd9d0d870db0
+    - path: output/unzip/versions.yml