From 8ef699294acfc343b6623de993ce40d3d5c4f8a4 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <matricaria.suaveolens@gmail.com>
Date: Wed, 3 Apr 2024 11:01:00 +0200
Subject: [PATCH] Add pigz module

---
 modules/nf-core/pigz/compress/environment.yml |  9 ++++
 modules/nf-core/pigz/compress/main.nf         | 45 +++++++++++++++++
 modules/nf-core/pigz/compress/meta.yml        | 47 ++++++++++++++++++
 .../nf-core/pigz/compress/tests/main.nf.test  | 49 +++++++++++++++++++
 .../pigz/compress/tests/main.nf.test.snap     | 37 ++++++++++++++
 modules/nf-core/pigz/compress/tests/tags.yml  |  2 +
 6 files changed, 189 insertions(+)
 create mode 100644 modules/nf-core/pigz/compress/environment.yml
 create mode 100644 modules/nf-core/pigz/compress/main.nf
 create mode 100644 modules/nf-core/pigz/compress/meta.yml
 create mode 100644 modules/nf-core/pigz/compress/tests/main.nf.test
 create mode 100644 modules/nf-core/pigz/compress/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/pigz/compress/tests/tags.yml

diff --git a/modules/nf-core/pigz/compress/environment.yml b/modules/nf-core/pigz/compress/environment.yml
new file mode 100644
index 00000000..7551d187
--- /dev/null
+++ b/modules/nf-core/pigz/compress/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "pigz_compress"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "pigz=2.8"
diff --git a/modules/nf-core/pigz/compress/main.nf b/modules/nf-core/pigz/compress/main.nf
new file mode 100644
index 00000000..152e7006
--- /dev/null
+++ b/modules/nf-core/pigz/compress/main.nf
@@ -0,0 +1,45 @@
+process PIGZ_COMPRESS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pigz:2.8':
+        'biocontainers/pigz:2.8' }"
+
+    input:
+    tuple val(meta), path(raw_file)
+
+    output:
+    tuple val(meta), path("$archive"), emit: archive
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    archive = raw_file.toString() + ".gz"
+    """
+    # Note: needs --stdout for pigz to avoid the following issue:
+    #   pigz: skipping: ${raw_file} is a symbolic link
+    pigz --processes $task.cpus --stdout --force ${args} ${raw_file} > ${archive}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz:\$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    archive = raw_file.toString() + ".gz"
+    """
+    touch ${archive}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz:\$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/pigz/compress/meta.yml b/modules/nf-core/pigz/compress/meta.yml
new file mode 100644
index 00000000..42efd735
--- /dev/null
+++ b/modules/nf-core/pigz/compress/meta.yml
@@ -0,0 +1,47 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pigz_compress"
+description: Compresses files with pigz.
+keywords:
+  - compress
+  - gzip
+  - parallelized
+tools:
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - raw_file:
+      type: file
+      description: File to be compressed
+      pattern: "*.*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - archive:
+      type: file
+      description: The compressed file
+      pattern: "*.gz"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@leoisl"
+maintainers:
+  - "@leoisl"
diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test b/modules/nf-core/pigz/compress/tests/main.nf.test
new file mode 100644
index 00000000..248d40fb
--- /dev/null
+++ b/modules/nf-core/pigz/compress/tests/main.nf.test
@@ -0,0 +1,49 @@
+nextflow_process {
+    name "Test Process PIGZ_COMPRESS"
+    script "../main.nf"
+    process "PIGZ_COMPRESS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pigz"
+    tag "pigz/compress"
+
+    test("sarscov2 - genome - fasta") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - genome - fasta - stub") {
+        options "-stub-run"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.archive[0][1]).name).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/pigz/compress/tests/main.nf.test.snap b/modules/nf-core/pigz/compress/tests/main.nf.test.snap
new file mode 100644
index 00000000..6e50456f
--- /dev/null
+++ b/modules/nf-core/pigz/compress/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "sarscov2 - genome - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ca30e9e1ffa1394ba7eefdac8cf3a3ad"
+                ],
+                "archive": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.fasta.gz:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ca30e9e1ffa1394ba7eefdac8cf3a3ad"
+                ]
+            }
+        ],
+        "timestamp": "2023-12-11T22:39:53.350546"
+    },
+    "sarscov2 - genome - fasta - stub": {
+        "content": [
+            "genome.fasta.gz"
+        ],
+        "timestamp": "2023-12-11T22:52:24.309192"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pigz/compress/tests/tags.yml b/modules/nf-core/pigz/compress/tests/tags.yml
new file mode 100644
index 00000000..42c46bfa
--- /dev/null
+++ b/modules/nf-core/pigz/compress/tests/tags.yml
@@ -0,0 +1,2 @@
+pigz/compress:
+  - "modules/nf-core/pigz/compress/**"