Add HTSLIB/BGZIPTABIX and deprecate redundant modules

modules/nf-core/bandage/image/tests/main.nf.test

@@ -9,7 +9,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "bandage"
     tag "bandage/image"
-    tag "tabix/bgzip"
+    tag "htslib/bgziptabix"
 
     test("test-bandage-image") {
 
@@ -41,14 +41,19 @@ nextflow_process {
     test("test-bandage-image - gzip") {
 
         setup {
-            run("TABIX_BGZIP"){
-                script "../../../tabix/bgzip/main.nf"
+            run("HTSLIB_BGZIPTABIX"){
+                script "../../../htslib/bgziptabix/main.nf"
                 process {
                     """
                     input[0] = [
     				    [ id:'B-3106' ], // meta map
-    				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true)
+    				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true),
+					[],
+					[]
     				]
+                    input[1] = "compress"
+                    input[2] = false
+                    input[3] = "gfa"
                     """
                 }
             }
@@ -57,7 +62,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = TABIX_BGZIP.out.output
+                input[0] = HTSLIB_BGZIPTABIX.out.output
                 """
             }
         }

modules/nf-core/custom/geneticmapconvert/tests/main.nf.test

@@ -10,7 +10,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "custom"
     tag "custom/geneticmapconvert"
-    tag "tabix/bgzip"
+    tag "htslib/bgziptabix"
 
     test("Convert map with pos\\tchr\\tcm - with header - meta.chr (glimpse format)") {
         when {
@@ -44,14 +44,19 @@ nextflow_process {
 
     test("Convert map with pos\\tchr\\tcM - with header - meta.chr (glimpse compressed format)") {
         setup {
-            run("TABIX_BGZIP"){
-                script "../../../tabix/bgzip/main.nf"
+            run("HTSLIB_BGZIPTABIX"){
+                script "../../../htslib/bgziptabix/main.nf"
                 process {
                     """
                     input[0] = [
                         [id: "test", chr:"chr21"],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map', checkIfExists: true),
+                        [],
+                        []
                     ]
+                    input[1] = "compress"
+                    input[2] = false
+                    input[3] = "map"
                     """
                 }
             }
@@ -62,7 +67,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = TABIX_BGZIP.out.output
+                input[0] = HTSLIB_BGZIPTABIX.out.output
                 """
             }
         }

modules/nf-core/htslib/bgziptabix/environment.yml

@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::htslib=1.23.1"
+  - "conda-forge::xz=5.8.3"

modules/nf-core/htslib/bgziptabix/main.nf

@@ -0,0 +1,88 @@
+process HTSLIB_BGZIPTABIX {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/33/33a1f2c7f36ec58339e41cbea096d121f606918778a91cfbef944b40ba7ce48b/data'
+        : 'community.wave.seqera.io/library/htslib_xz:49c8c84af5c4b3b9'}"
+
+    input:
+    tuple val(meta), path(infile), path(infile_tbi), path(regions)
+    val action
+    val make_index
+    val out_ext
+
+    output:
+    tuple val(meta), path("${outfile}"), emit: output
+    tuple val(meta), path("${outfile}.{tbi,csi}"), emit: index, optional: true
+    // all htslib tools have the same version, we use bgzip
+    tuple val("${task.process}"), val('htslib'), eval("bgzip --version | sed '1! d; s/bgzip (htslib) //'"), topic: versions, emit: versions_htslib
+    tuple val("${task.process}"), val('xz'), eval("xz --version | sed '1! d; s/xz (XZ Utils) //'"), topic: versions, emit: versions_xz
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def allowed_actions = ["compress", "decompress"]
+    if (action !in allowed_actions) {
+        error("htslib/bgziptabix: Invalid action: ${action}. Allowed actions are: ${allowed_actions.join(', ')}")
+    }
+
+    if (action == "decompress" && make_index) {
+        log.warn("htslib/bgziptabix: Cannot create index when decompressing. Ignoring make_index option.")
+    }
+
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    outfile = action == "compress" ? (out_ext ? "${prefix}.${out_ext}.gz" : "${prefix}.gz") : (out_ext ? "${prefix}.${out_ext}" : "${prefix}")
+
+    def compress_cmd = action == "compress" ? "bgzip -c ${args} -@ ${task.cpus}" : "cat"
+    def bgzip_cmd = action == "compress" ? "[ '\$(basename ${infile})' != '\$(basename ${outfile})' ] && ln -s ${infile} ${outfile}" : "bgzip -c -d ${args} -@ ${task.cpus} ${infile} > ${outfile}"
+
+    def regions_arg = regions ? "-R ${regions}" : ""
+    def tabix_cmd = (make_index && !infile_tbi) ? "tabix -@ ${task.cpus} ${regions_arg} ${args2} -f ${outfile}" : ""
+    def link_tabix_cmd = make_index && infile_tbi ? "ln -s ${infile_tbi} ${outfile}.${infile_tbi.extension}" : ""
+    def uncompressed_cmd = action == "compress" ? "${compress_cmd} ${infile} > ${outfile}" : (infile.getName() == outfile ? "" : "ln -s ${infile} ${outfile}")
+    """
+    ${link_tabix_cmd}
+
+    FILE_TYPE=\$(htsfile ${infile})
+
+    case "\$FILE_TYPE" in
+        *BGZF-compressed*)
+            ${bgzip_cmd} ;;
+        *gzip-compressed*)
+            [ "\$(basename ${infile})" == "\$(basename ${outfile})" ] && echo "Input and output names cannot be the same" && exit 1
+            zcat  ${infile} | ${compress_cmd} > ${outfile} ;;
+        *bzip2-compressed*)
+            bzcat ${infile} | ${compress_cmd} > ${outfile} ;;
+        *XZ-compressed*)
+            xzcat ${infile} | ${compress_cmd} > ${outfile} ;;
+        *)
+            ${uncompressed_cmd} ;;
+    esac
+
+    ${tabix_cmd}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    outfile = action == "compress" ? (out_ext ? "${prefix}.${out_ext}.gz" : "${prefix}.gz") : (out_ext ? "${prefix}.${out_ext}" : "${prefix}")
+
+    def touch_cmd = action == "compress" ? "echo | bgzip -c" : "echo"
+    def index_fmt = args2.contains('-C') ? 'csi' : 'tbi'
+    def tabix_cmd = make_index ? "touch ${outfile}.${index_fmt}" : ""
+    def link_tabix_cmd = make_index && infile_tbi ? "ln -s ${infile_tbi} ${outfile}.${infile_tbi.extension}" : ""
+    """
+    echo ${args}
+
+    ${touch_cmd} > ${outfile}
+
+    ${tabix_cmd}
+    ${link_tabix_cmd}
+    """
+}

modules/nf-core/htslib/bgziptabix/meta.yml

@@ -0,0 +1,125 @@
+name: "htslib_bgziptabix"
+description: "Multi-purpose module to compress, decompress and index files using bgzip
+  and tabix."
+keywords:
+  - compress
+  - decompress
+  - index
+  - bgzip
+  - tabix
+  - gzip
+  - bzip
+  - xz
+tools:
+  - "htslib":
+      description: "C library for high-throughput sequencing data formats."
+      homepage: "http://www.htslib.org/"
+      documentation: "http://www.htslib.org/doc/"
+      tool_dev_url: "https://github.com/samtools/htslib"
+      doi: "10.1093/gigascience/giab007"
+      licence:
+        - "MIT"
+      identifier: biotools:htslib
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'sample1' ]
+    - infile:
+        type: file
+        description: Input file to compress or decompress
+        pattern: "*"
+        ontologies: []
+    - infile_tbi:
+        type: file
+        description: Optional tabix index for the input file.
+        pattern: "*.{tbi,csi}"
+        ontologies:
+          - edam: http://edamontology.org/format_3616 # tabix
+    - regions:
+        type: file
+        description: Optional file of regions to extract (BED or chr:start-end format).
+          Only used when creating an index for the output file.
+        pattern: "*.{bed,txt,tsv}"
+        ontologies:
+          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3003 # BED
+  - action:
+      type: string
+      description: Action to perform, either `compress` or `decompress`
+  - make_index:
+      type: boolean
+      description: Whether to create a tabix index for the output file; only used
+        if `action` is `compress`
+  - out_ext:
+      type: string
+      description: Output file extension without `.gz` suffix (for example `vcf`)
+output:
+  output:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1' ]
+      - ${outfile}:
+          type: file
+          description: Compressed or decompressed output file
+          pattern: "*"
+          ontologies: []
+  index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1' ]
+      - ${outfile}.{tbi,csi}:
+          type: file
+          description: Tabix index file for the compressed output file
+          pattern: "*.{tbi,csi}"
+          ontologies:
+            - edam: http://edamontology.org/format_3616 # tabix
+  versions_htslib:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - htslib:
+          type: string
+          description: The name of the tool
+      - bgzip --version | sed '1! d; s/bgzip (htslib) //':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_xz:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - xz:
+          type: string
+          description: The name of the tool
+      - xz --version | sed '1! d; s/xz (XZ Utils) //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - htslib:
+          type: string
+          description: The name of the tool
+      - bgzip --version | sed '1! d; s/bgzip (htslib) //':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - xz:
+          type: string
+          description: The name of the tool
+      - xz --version | sed '1! d; s/xz (XZ Utils) //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@itrujnara"
+maintainers:
+  - "@itrujnara"