new module: crabz (#5351)

* feat: add crabz skeleton

* feat: update `environment.yml`

* feat: add crabz version

* feat: add `crabz` to `container`

* fix: update label

* feat: update `CRABZ_COMPRESS` process

* WIP: add `CRABZ_DECOMPRESS` process

* fix: stub run

* fix: update file paths

* fix: update snapshot

* fix: tool name

* fix: remove unused `--quiet` flag

modules/nf-core/crabz/compress/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "crabz_compress"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::crabz=0.9.0

modules/nf-core/crabz/compress/main.nf

@@ -0,0 +1,49 @@
+process CRABZ_COMPRESS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/crabz:0.9.0':
+        'biocontainers/crabz:0.9.0' }"
+
+    input:
+    tuple val(meta), path(file)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: archive
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${file}"
+    """
+    crabz \\
+        $args \\
+        -p $task.cpus \\
+        -o ${prefix}.gz \\
+        $file
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabz: \$(crabz --version |& sed 's/[^:]*://')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${file}"
+    """
+    echo "" | gzip > ${prefix}.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabz: \$(crabz --version |& sed 's/[^:]*://')
+
+
+    END_VERSIONS
+    """
+}

modules/nf-core/crabz/compress/meta.yml

@@ -0,0 +1,50 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "crabz_compress"
+description: Compress files with crabz
+keywords:
+  - compression
+  - gzip
+  - zlib
+tools:
+  - crabz:
+      description: "Like pigz, but rust"
+      homepage: "https://github.com/sstadick/crabz"
+      documentation: "https://github.com/sstadick/crabz"
+      tool_dev_url: "https://github.com/sstadick/crabz"
+      licence: ["MIT"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - file:
+      type: file
+      description: File to be compressed
+      pattern: "*.*"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - archive:
+      type: file
+      description: The compressed file
+      pattern: "*.gz"
+
+authors:
+  - "@camlloyd"
+maintainers:
+  - "@camlloyd"

modules/nf-core/crabz/compress/tests/main.nf.test

@@ -0,0 +1,61 @@
+nextflow_process {
+
+    name "Test Process CRABZ_COMPRESS"
+    script "../main.nf"
+    process "CRABZ_COMPRESS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "crabz"
+    tag "crabz/compress"
+
+    test("sarscov2 - genome - fasta") {
+
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/crabz/compress/tests/tags.yml

@@ -0,0 +1,2 @@
+crabz/compress:
+  - "modules/nf-core/crabz/compress/**"

modules/nf-core/crabz/decompress/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "crabz_decompress"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::crabz=0.9.0

modules/nf-core/crabz/decompress/main.nf

@@ -0,0 +1,47 @@
+process CRABZ_DECOMPRESS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/crabz:0.9.0':
+        'biocontainers/crabz:0.9.0' }"
+
+    input:
+    tuple val(meta), path(archive)
+
+    output:
+    tuple val(meta), path("*.*"), emit: file
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${archive}"
+    """
+    crabz \\
+        $args \\
+        -p $task.cpus \\
+        -o ${prefix} \\
+        $archive
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabz: \$(crabz --version |& sed 's/[^:]*://')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${archive}"
+    """
+    touch ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabz: \$(crabz --version |& sed 's/[^:]*://')
+    END_VERSIONS
+    """
+}

modules/nf-core/crabz/decompress/meta.yml

@@ -0,0 +1,50 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "crabz_decompress"
+description: Decompress files with crabz
+keywords:
+  - decompression
+  - gzip
+  - zlib
+tools:
+  - crabz:
+      description: "Like pigz, but rust"
+      homepage: "https://github.com/sstadick/crabz"
+      documentation: "https://github.com/sstadick/crabz"
+      tool_dev_url: "https://github.com/sstadick/crabz"
+      licence: ["MIT"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - archive:
+      type: file
+      description: File to be decompressed
+      pattern: "*.gz"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - file:
+      type: file
+      description: The decompressed file
+      pattern: "*.*"
+
+authors:
+  - "@camlloyd"
+maintainers:
+  - "@camlloyd"