Pigzip (nf-core#4156)

* compress workflow

* add compress tests to pytest

* fix

* uncompress

* uncompress tests

* Revert "uncompress tests", will do nf-tests

This reverts commit 6e7a33e.

* Revert "add compress tests to pytest", will do nf-tests

This reverts commit 139e5c2.

* generating the nf-tests for the processes

* first test written, need actual run

* set stageInMode

* call -f to make pigz follow symlinks

* uncompress keeps input

* remove compress module

* written first iteration of nf-test for pigz/uncompress

* empty line in tag.yml

* adding missing tags in main.nf.test and fixed linting errors

* add old singularity container for pigz

* switch from pgzip to pigz singularity/biocontainers container, in anticipation of BioContainers/multi-package-containers#2793 being merged

---------

Co-authored-by: Leon Rauschning <[email protected]>
Co-authored-by: alessiovignoli <[email protected]>

modules/nf-core/pigz/uncompress/main.nf

@@ -0,0 +1,48 @@
+process PIGZ_UNCOMPRESS {
+    label 'process_low'
+    //stageInMode 'copy' // this directive can be set in case the original input should be kept
+
+    conda "conda-forge::pigz"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pigz:2.8':
+        'biocontainers/pigz:2.8' }"
+
+    input:
+    path zip
+
+    output:
+    path "${uncompressed_filename}" , emit: file
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    uncompressed_filename = zip.toString() - '.gz'
+    // calling pigz -f to make it follow symlinks
+    """
+    unpigz \\
+        -p $task.cpus \\
+        -fk \\
+        $args \\
+        ${zip}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    uncompressed_filename = zip.toString() - '.gz'
+    """
+    touch ${zip.dropRight(3)}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\w*//' ))
+    END_VERSIONS
+    """
+}

modules/nf-core/pigz/uncompress/meta.yml

@@ -0,0 +1,32 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "pigz_uncompress"
+description: write your description here
+keywords:
+  - uncompress
+  - gzip
+  - parallelized
+tools:
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
+
+input:
+  - zip:
+      type: file
+      description: Gzipped file
+      pattern: "*.{gzip}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - file:
+      type: file
+      description: File to compress
+      pattern: "*"
+
+authors:
+  - "@lrauschning"

modules/nf-core/pigz/uncompress/tests/main.nf.test

@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process PIGZ_UNCOMPRESS"
+    script "modules/nf-core/pigz/uncompress/main.nf"
+    process "PIGZ_UNCOMPRESS"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pigz"
+    tag "pigz/uncompress"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                                file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

modules/nf-core/pigz/uncompress/tests/tags.yml

@@ -0,0 +1,2 @@
+pigz/uncompress:
+  - modules/nf-core/pigz/uncompress/**