Module to download CDD databases

modules/nf-core/blast/cdddownloader/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gnu-wget=1.18

modules/nf-core/blast/cdddownloader/main.nf

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+process BLAST_CDDDOWNLOADER {
+    tag "$db_prefix"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9'
+        : 'biocontainers/gnu-wget:1.18--h36e9172_9'}"
+
+    input:
+    val db_prefix
+
+    output:
+    path "cdd_databases/", emit: db
+    tuple val("${task.process}"), val('wget'), eval("wget --version | head -1 | cut -d ' ' -f 3"), topic: versions, emit: versions_wget
+    tuple val("${task.process}"), val('untar'), eval("tar --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -1"), topic: versions, emit: versions_tar
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def db_name = 'Cdd_NCBI_LE'
+    if ( "$db_prefix" ==~ /^Cdd$/ ) {
+        db_name = 'Cdd_LE'
+    } else if ( "$db_prefix" ==~ /^Cog$/ ) {
+        db_name = 'Cog_LE'
+    } else if ( "$db_prefix" ==~ /^Kog$/ ) {
+        db_name = 'Kog_LE'
+    } else if ( "$db_prefix" ==~ /^Pfam$/ ) {
+        db_name = 'Pfam_LE'
+    } else if ( "$db_prefix" ==~ /^Prk$/ ) {
+        db_name = 'Prk_LE'
+    } else if ( "$db_prefix" ==~ /^Smart$/ ) {
+        db_name = 'Smart_LE'
+    } else if ( "$db_prefix" ==~ /^Tigr$/ ) {
+        db_name = 'Tigr_LE'
+    } else {
+        log.warn("Unknown CDD databse name (${db_prefix}): selecting Cdd_NCBI default of downloading")
+        db_prefix = 'Cdd_NCBI'
+    }
+
+    """
+    mkdir -p cdd_databases/${db_prefix}
+    cd cdd_databases/
+    mkdir data
+
+    echo "Downloading ${db_prefix} database into ${db_prefix} dir"
+
+    wget https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/${db_name}.tar.gz
+    tar -xzf ${db_name}.tar.gz -C ./${db_prefix}
+    rm -f ${db_name}.tar.gz
+
+    echo "Downloading metadata files"
+
+    wget https://ftp.ncbi.nih.gov/pub/mmdb/cdd/cddid.tbl.gz -O ./data/cddid.tbl.gz && gzip -d ./data/cddid.tbl.gz
+    wget https://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdtrack.txt -O ./data/cdtrack.txt
+    wget https://ftp.ncbi.nih.gov/pub/mmdb/cdd/family_superfamily_links -O ./data/family_superfamily_links
+    wget https://ftp.ncbi.nih.gov/pub/mmdb/cdd/cddannot.dat.gz -O ./data/cddannot.dat.gz && gzip -d ./data/cddannot.dat.gz
+    wget https://ftp.ncbi.nih.gov/pub/mmdb/cdd/cddannot_generic.dat.gz -O ./data/cddannot_generic.dat.gz && gzip -d ./data/cddannot_generic.dat.gz
+    wget https://ftp.ncbi.nih.gov/pub/mmdb/cdd/bitscore_specific.txt -O ./data/bitscore_specific.txt
+
+    echo "Finish"
+
+    """
+
+    stub:
+    """
+    mkdir cdd_databases/
+    """
+}

modules/nf-core/blast/cdddownloader/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "blast_cdddownloader"
+description: CDD databases downloader
+keywords:
+  - cdd
+  - rpsblast
+  - databases
+  - metadata
+  - wget
+  - tar
+tools:
+  - wget:
+      description: "wget is a free utility for non-interactive download of files from
+        the Web."
+      homepage: "https://www.gnu.org/software/wget/"
+      documentation: "https://www.gnu.org/software/wget/manual/wget.html"
+      licence: ["GPL"]
+      identifier: ""
+  - untar:
+      description: |
+        Extract tar, tar.gz, tar.bz2, tar.xz files.
+      documentation: https://www.gnu.org/software/tar/manual/
+      licence: ["GPL-3.0-or-later"]
+      identifier: ""
+input:
+  - db_prefix:
+      type: string
+      description: |
+        Specify the database to be downloaded from https://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
+      pattern: "Cdd|Cdd_NCBI|Cog|Kog|Pfam|Prk|Smart|Tigr"
+output:
+  db:
+    - cdd_databases/:
+        type: directory
+        description: Directory containing the CDD database files
+        pattern: "cdd_databases/"
+  versions_wget:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - wget:
+          type: string
+          description: The name of the tool
+      - wget --version | head -1 | cut -d ' ' -f 3:
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_tar:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - untar:
+          type: string
+          description: The name of the tool
+      - tar --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -1:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - wget:
+          type: string
+          description: The name of the tool
+      - wget --version | head -1 | cut -d ' ' -f 3:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@Ales-ibt"
+maintainers:
+  - "@Ales-ibt"

modules/nf-core/blast/cdddownloader/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process BLAST_CDDDOWNLOADER"
+    script "../main.nf"
+    process "BLAST_CDDDOWNLOADER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "blast"
+    tag "blast/cdddownloader"
+
+    test("cdddownload - smart") {
+        when {
+            process {
+                """
+                input[0] = 'Smart'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.db,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+    test("cdddownload - default Cdd_NCBI") {
+        when {
+            process {
+                """
+                input[0] = ''
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.db,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+    test("cdddownload - smart - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = 'Smart'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.db,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+    test("cdddownload - default Cdd_NCBI - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = ''
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out.db,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+}