New samtools/bgzip module to produce BGZF-compressed files.

modules/nf-core/samtools/bgzip/environment.yml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::samtools=1.21
+  - conda-forge::file=5.46

modules/nf-core/samtools/bgzip/main.nf

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+process SAMTOOLS_BGZIP {
+    tag "$fasta"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/61/61be440cd54169fcefe5303238847dd466728453a130f4fbc5abd68b514f0b09/data' :
+        'community.wave.seqera.io/library/samtools_file:f35ca613dd912bed' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path ("*.bgzip.fa.gz") , emit: fa
+    path "versions.yml"                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    COMPRESS_TYPE=\$(file -L -b $fasta)
+
+    case "\$COMPRESS_TYPE" in
+        "gzip compressed data, extra field"*)
+            # A well-behaved find installation should report:
+            # Blocked GNU Zip Format (BGZF; gzip compatible)
+            # But the one in anaconda does nt…
+            # Assuming the "extra field" implies BGZF, do nothing.
+            ln -s $fasta ${prefix}.bgzip.fa.gz
+            ;;
+        gzip*)
+            # Recompress non-BGZF gzipped files
+            zcat $fasta |
+                bgzip \\
+                    $args \\
+                    --threads ${task.cpu} \\
+                    > ${prefix}.bgzip.fa.gz
+            ;;
+        *)
+            # Compress
+            bgzip \\
+                $args \\
+                --threads ${task.cpu} \\
+                --stdout \\
+                $fasta \\
+                > ${prefix}.bgzip.fa.gz
+            ;;
+    esac
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        file: \$(echo \$(file --version 2>&1 | head -n1 | sed 's/file-//'))
+        samtools: \$(echo \$(samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //; s/Using.*\$//'))
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo '' | bgzip > ${prefix}.bgzip.fa.gz
+
+    cat <<-END_VERSIONS > versions.yml
+
+    "${task.process}":
+        file: \$(echo \$(file --version 2>&1 | head -n1 | sed 's/file-//'))
+        samtools: \$(echo \$(samtools --version 2>&1 | head -n1 | sed 's/^.*samtools //; s/Using.*\$//'))
+    END_VERSIONS
+    """
+}

modules/nf-core/samtools/bgzip/meta.yml

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+name: samtools_bgzip
+description: Produce a FASTA file compressed with the BGZF algorithm
+keywords:
+  - fasta
+  - BGZF
+  - bgzip
+tools:
+  - file:
+      description: |
+        The file command is "a file type guesser", that is, a command-line tool that tells you
+        in words what kind of data a file contains. Unlike most GUI systems, command-line UNIX
+        systems - with this program leading the charge - don't rely on filename extentions to
+        tell you the type of a file, but look at the file's actual contents. This is, of course,
+        more reliable, but requires a bit of I/O.
+      homepage: https://www.darwinsys.com/file/
+      documentation: https://manpages.debian.org/bookworm/file/file.1.en.html
+      licence: ["BSD-2-clause"]
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:samtools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: FASTA file, compressed or not.
+        pattern: "*.{fa,fa.gz,fasta,fasta.gz}"
+output:
+  - fa:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bgzip.fa.gz":
+          type: file
+          description: |
+            A FASTA file compressed with the BGZF algorithm.  It will be
+            the original file if it was already BGZF-compressed.
+          pattern: "*.{bgzip.fa.gz}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@charles-plessy"
+maintainers:
+  - "@charles-plessy"

modules/nf-core/samtools/bgzip/tests/main.nf.test

@@ -0,0 +1,89 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_BGZIP"
+    script "../main.nf"
+    process "SAMTOOLS_BGZIP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/bgzip"
+
+    test("test_samtools_bgzip - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // 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("test_samtools_bgzip - fasta bgzipped") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_bgzip - proteome gzipped") {
+    // This file is not bgziped. It is used to check the re-zipping branch of the case statement in the module.
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_samtools_bgzip - fasta stub") {
+
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // 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/samtools/bgzip/tests/main.nf.test.snap

@@ -0,0 +1,142 @@
+{
+    "test_samtools_bgzip - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dcbb9ab7afbb0348506d508dac612f9a"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dcbb9ab7afbb0348506d508dac612f9a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-05T16:22:43.985034"
+    },
+    "test_samtools_bgzip - fasta bgzipped": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dcbb9ab7afbb0348506d508dac612f9a"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dcbb9ab7afbb0348506d508dac612f9a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-05T16:22:59.160449"
+    },
+    "test_samtools_bgzip - fasta stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,18b35ac93df8e34bed8e6c086d6394c4"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,18b35ac93df8e34bed8e6c086d6394c4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-05T16:23:28.612494"
+    },
+    "test_samtools_bgzip - proteome gzipped": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,db0ecd5dbce6bf9730685b94ec87854d"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dcbb9ab7afbb0348506d508dac612f9a"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bgzip.fa.gz:md5,db0ecd5dbce6bf9730685b94ec87854d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dcbb9ab7afbb0348506d508dac612f9a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-05T16:23:13.752005"
+    }
+}

modules/nf-core/samtools/bgzip/tests/tags.yml

@@ -0,0 +1,2 @@
+samtools/bgzip:
+  - modules/nf-core/samtools/bgzip/**