From 0cd67d7b40b5e811a8774e22d27f417d7c1c1e5d Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Wed, 17 Dec 2025 15:40:59 +0000
Subject: [PATCH 01/15] Module to dowload CDD databases

---
 .../blast/cdddownloader/environment.yml       |   7 +
 modules/nf-core/blast/cdddownloader/main.nf   |  70 +++++
 modules/nf-core/blast/cdddownloader/meta.yml  |  77 ++++++
 .../blast/cdddownloader/tests/main.nf.test    | 102 +++++++
 .../cdddownloader/tests/main.nf.test.snap     | 249 ++++++++++++++++++
 5 files changed, 505 insertions(+)
 create mode 100644 modules/nf-core/blast/cdddownloader/environment.yml
 create mode 100644 modules/nf-core/blast/cdddownloader/main.nf
 create mode 100644 modules/nf-core/blast/cdddownloader/meta.yml
 create mode 100644 modules/nf-core/blast/cdddownloader/tests/main.nf.test
 create mode 100644 modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap

diff --git a/modules/nf-core/blast/cdddownloader/environment.yml b/modules/nf-core/blast/cdddownloader/environment.yml
new file mode 100644
index 000000000000..2a5094dc4823
--- /dev/null
+++ b/modules/nf-core/blast/cdddownloader/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gnu-wget=1.18
diff --git a/modules/nf-core/blast/cdddownloader/main.nf b/modules/nf-core/blast/cdddownloader/main.nf
new file mode 100644
index 000000000000..1059458dd027
--- /dev/null
+++ b/modules/nf-core/blast/cdddownloader/main.nf
@@ -0,0 +1,70 @@
+process BLAST_CDDDOWNLOADER {
+    tag "$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/
+    """
+}
diff --git a/modules/nf-core/blast/cdddownloader/meta.yml b/modules/nf-core/blast/cdddownloader/meta.yml
new file mode 100644
index 000000000000..ef9070d0adac
--- /dev/null
+++ b/modules/nf-core/blast/cdddownloader/meta.yml
@@ -0,0 +1,77 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "blast_cdddownloader"
+description: CDD databases downloader
+keywords:
+  - cdd
+  - rpsblast
+  - databases
+  - metadata
+  - wget
+  - tar
+tools:
+  - wget:
+      description: "wget is a free utility for non-interactive download of files from
+        the Web."
+      homepage: "https://www.gnu.org/software/wget/"
+      documentation: "https://www.gnu.org/software/wget/manual/wget.html"
+      licence: ["GPL"]
+      identifier: ""
+  - untar:
+      description: |
+        Extract tar, tar.gz, tar.bz2, tar.xz files.
+      documentation: https://www.gnu.org/software/tar/manual/
+      licence: ["GPL-3.0-or-later"]
+      identifier: ""
+input:
+  - db_prefix:
+      type: string
+      description: |
+        Specify the database to be downloaded from https://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
+      pattern: "Cdd|Cdd_NCBI|Cog|Kog|Pfam|Prk|Smart|Tigr"
+output:
+  db:
+    - cdd_databases:
+        type: directory
+        description: Directory containing the CDD database
+        pattern: "cdd_databases"
+  versions_wget:
+    - - "${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
+      - tar:
+          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
+authors:
+  - "@Ales-ibt"
+maintainers:
+  - "@Ales-ibt"
diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test b/modules/nf-core/blast/cdddownloader/tests/main.nf.test
new file mode 100644
index 000000000000..0b501cbaa417
--- /dev/null
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test
@@ -0,0 +1,102 @@
+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() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
new file mode 100644
index 000000000000..3918fcf93af4
--- /dev/null
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -0,0 +1,249 @@
+{
+    "cdddownload - default Cdd_NCBI": {
+        "content": [
+            [
+                [
+                    [
+                        "Cdd_NCBI.00.aux:md5,2cf6cb9f7f0ef642384d8c14cba3e082",
+                        "Cdd_NCBI.00.freq:md5,4c59913079f18de0f77f4cc8788bdd13",
+                        "Cdd_NCBI.00.loo:md5,bcbe57d5675dc672d4cba582e1278cbe",
+                        "Cdd_NCBI.00.pdb:md5,a1b54a4094f894b0f0cfa1569c4349fc",
+                        "Cdd_NCBI.00.phr:md5,3e7853e6e55ff5a989d4fadbe2c9212e",
+                        "Cdd_NCBI.00.pin:md5,e98d522a0bf488fe1cded992f0a210c6",
+                        "Cdd_NCBI.00.pos:md5,f035257d2cf8b7c604af184fc0a1f572",
+                        "Cdd_NCBI.00.pot:md5,585036ed381f809ea3f4b786a8becfe3",
+                        "Cdd_NCBI.00.psq:md5,1f2c97538c619a3d69a93a42c1bd92c0",
+                        "Cdd_NCBI.00.ptf:md5,cb0bb0df9175d18dc10dd272bd1c2d73",
+                        "Cdd_NCBI.00.pto:md5,df60428e450170375d847fdcd150e010",
+                        "Cdd_NCBI.00.rps:md5,cbd40f7ab89616ad0af3437ba71cec4d",
+                        "Cdd_NCBI.01.aux:md5,480132803643efc067d7c6f152174d91",
+                        "Cdd_NCBI.01.freq:md5,d59c89f4d02b98fe62a946a40321aff5",
+                        "Cdd_NCBI.01.loo:md5,fe5379e3ebc440bb407363a38f7d542f",
+                        "Cdd_NCBI.01.pdb:md5,6120c94ce34efdeb0258fba25125f961",
+                        "Cdd_NCBI.01.phr:md5,dc8d17f1698cd7b518de5753ddc075b2",
+                        "Cdd_NCBI.01.pin:md5,c2a030d3ca4a7a81c806f5944f29f1c9",
+                        "Cdd_NCBI.01.pos:md5,30cbaa24e160c8b601724c883e7f3bb1",
+                        "Cdd_NCBI.01.pot:md5,ac3d1ad2972b44599d9dd1fc5378cac3",
+                        "Cdd_NCBI.01.psq:md5,8df5eca3148179fa06eec5fe033fae0e",
+                        "Cdd_NCBI.01.ptf:md5,389e824f6df828fc315e2724732d7d4b",
+                        "Cdd_NCBI.01.pto:md5,4eb459a5d52852e349040cf724984aa0",
+                        "Cdd_NCBI.01.rps:md5,9466094c94ab9b11b690a47116024419",
+                        "Cdd_NCBI.02.aux:md5,82eaa7e9aae83ee82069d9edc1c39265",
+                        "Cdd_NCBI.02.freq:md5,057a498514f177c30ec8644fadbacf87",
+                        "Cdd_NCBI.02.loo:md5,92a419c852dbc0dc922a7569201d8b73",
+                        "Cdd_NCBI.02.pdb:md5,991d4e3500285fdd79782268967798f9",
+                        "Cdd_NCBI.02.phr:md5,700bf513563027421278e9b55ebcb447",
+                        "Cdd_NCBI.02.pin:md5,a078fdf12716070c1886a5a9b7f49e85",
+                        "Cdd_NCBI.02.pos:md5,66bdddc0fadf5f2f5b748e3cd2dcbdd2",
+                        "Cdd_NCBI.02.pot:md5,f23332ad9e27d78a43d668268da6ad88",
+                        "Cdd_NCBI.02.psq:md5,0b155fc0b9c4ef3359ee9279e5ddfbb8",
+                        "Cdd_NCBI.02.ptf:md5,311588ec68aaad59c053b9632a7e6002",
+                        "Cdd_NCBI.02.pto:md5,5a57bf533a61447d98dc4333cc3754e5",
+                        "Cdd_NCBI.02.rps:md5,ef77d8943522f4c159edde876d5c587b",
+                        "Cdd_NCBI.03.aux:md5,a59087a1ae991fe2c6b0ae6fc9c8f005",
+                        "Cdd_NCBI.03.freq:md5,b2e0afdcb93f9d3b3eaadeeb2e5f0193",
+                        "Cdd_NCBI.03.loo:md5,045cb2a75a56012f86681b680b5de751",
+                        "Cdd_NCBI.03.pdb:md5,0c2021397e6daae4f356bb9a58f53e71",
+                        "Cdd_NCBI.03.phr:md5,c9800c3a7d68e0621f1ce797c86b05fc",
+                        "Cdd_NCBI.03.pin:md5,7873b2b62611338e8356c6e29f8bb116",
+                        "Cdd_NCBI.03.pos:md5,a20343bdff20d95ba97ba8005b45141e",
+                        "Cdd_NCBI.03.pot:md5,22958ea67bfd015e1cb3b02e0017b6e6",
+                        "Cdd_NCBI.03.psq:md5,fccffe1be7cf46ebe72316c7096ff01f",
+                        "Cdd_NCBI.03.ptf:md5,440863b30ed135e65bf6cb9ac9491a42",
+                        "Cdd_NCBI.03.pto:md5,1bef0988747ad4755a71995cb95c971f",
+                        "Cdd_NCBI.03.rps:md5,1165ef5a319b642b9ad61211194dca6f",
+                        "Cdd_NCBI.04.aux:md5,38a366bd85895d99838e35ce088229dc",
+                        "Cdd_NCBI.04.freq:md5,4144c80db0cb99f529f264a6f09f09f9",
+                        "Cdd_NCBI.04.loo:md5,3b60b2314395e63fa68ce13c54b04952",
+                        "Cdd_NCBI.04.pdb:md5,e61e8caa24644465c74d9b0658555d43",
+                        "Cdd_NCBI.04.phr:md5,27456857457af9d7dba0f144e7ee97bb",
+                        "Cdd_NCBI.04.pin:md5,6241ff613a80b6661f48ba8d3a444da5",
+                        "Cdd_NCBI.04.pos:md5,7f073d8d616d85aaba4574056fe46910",
+                        "Cdd_NCBI.04.pot:md5,c8970b13dab458ead44a8a21d0f8d79a",
+                        "Cdd_NCBI.04.psq:md5,819c9df385960414e762992c54db70ae",
+                        "Cdd_NCBI.04.ptf:md5,09cc415f6b53b7781e41cdf8926bd7ef",
+                        "Cdd_NCBI.04.pto:md5,5ee7a4999a5fba7e841936086b6b689c",
+                        "Cdd_NCBI.04.rps:md5,5b7963dce4d05a7ebe151968ec522189",
+                        "Cdd_NCBI.05.aux:md5,1b1252353d7bcacb680a0a27538446e0",
+                        "Cdd_NCBI.05.freq:md5,3ddb8314cfbc474651d43ba463d76d39",
+                        "Cdd_NCBI.05.loo:md5,dbaefdf36c9569c5361b67d76bd86168",
+                        "Cdd_NCBI.05.pdb:md5,0380f49d2f0ba624051e4fab37719baf",
+                        "Cdd_NCBI.05.phr:md5,8af691e75da9496b477e88b3aab4f3c3",
+                        "Cdd_NCBI.05.pin:md5,5acb72e95d93255d945f9adf1052ebb7",
+                        "Cdd_NCBI.05.pos:md5,c1e4800d6bdf8272c4ec4df874c7650e",
+                        "Cdd_NCBI.05.pot:md5,d0eb2c5fa062b7129578ecc338276ce3",
+                        "Cdd_NCBI.05.psq:md5,f73358e4e01b2125eb1c285b405ab04b",
+                        "Cdd_NCBI.05.ptf:md5,544145576ccada56a977d02c50881f84",
+                        "Cdd_NCBI.05.pto:md5,32c711282c2288929a0819551798c73d",
+                        "Cdd_NCBI.05.rps:md5,1f2e7971ea96aae3f3ac42d7e2cd64a3",
+                        "Cdd_NCBI.06.aux:md5,6bab8ea4135a084f711db51424a781b7",
+                        "Cdd_NCBI.06.freq:md5,9deffbbc581705be20a4edf9f9d18931",
+                        "Cdd_NCBI.06.loo:md5,ad399b7414b4df9062a59e8c1c22239a",
+                        "Cdd_NCBI.06.pdb:md5,1767c49a25c6425496a4db3101fe2ca6",
+                        "Cdd_NCBI.06.phr:md5,48b2c5496974f0c85af1716c2e8e41a0",
+                        "Cdd_NCBI.06.pin:md5,3d5c7b9f5b9494c36b0f1fc35196277a",
+                        "Cdd_NCBI.06.pos:md5,450b0b415e47a7ccce9159995a0d822a",
+                        "Cdd_NCBI.06.pot:md5,2771d84055bef1860f4212caa4586d4b",
+                        "Cdd_NCBI.06.psq:md5,e2e4a4288a0b9cc67a3d3cdbe3e72425",
+                        "Cdd_NCBI.06.ptf:md5,fdf6de6fb97b5cf8b1e51c9a09bc3d28",
+                        "Cdd_NCBI.06.pto:md5,f8bf44b73a2cd109c268bcb555801f90",
+                        "Cdd_NCBI.06.rps:md5,84580c4a449fa1b757e50ac8a074b6d5",
+                        "Cdd_NCBI.07.aux:md5,5d4747b8272336053367be85e2972d0b",
+                        "Cdd_NCBI.07.freq:md5,45b8462efb9d5d618a6ae943e8af7f28",
+                        "Cdd_NCBI.07.loo:md5,370c54250d3495016427f94ba974899a",
+                        "Cdd_NCBI.07.pdb:md5,cccd58c9fdfd72b40bf5666f8611667a",
+                        "Cdd_NCBI.07.phr:md5,45effa854f58a243453f45603abf7034",
+                        "Cdd_NCBI.07.pin:md5,7e95ce44f30f8d039c1c35eced8fe293",
+                        "Cdd_NCBI.07.pos:md5,50692f4e27addd95315514bdaa6a4c29",
+                        "Cdd_NCBI.07.pot:md5,e061ac1e37c4b32311d9e84464387f75",
+                        "Cdd_NCBI.07.psq:md5,8b8621e1a2f0732cec898bd79ab66158",
+                        "Cdd_NCBI.07.ptf:md5,a3b39fa3de11646a1f223822ee68f7a6",
+                        "Cdd_NCBI.07.pto:md5,e4f05bce8df339e8eec50b12c143bb83",
+                        "Cdd_NCBI.07.rps:md5,dd8ff67c2524f9d301272d323542ce41",
+                        "Cdd_NCBI.pal:md5,a641307f32eff5e6a44c4a040f2a37fd"
+                    ],
+                    [
+                        "bitscore_specific.txt:md5,417ab1c1223f42a38cb4c0caee8165f5",
+                        "cddannot.dat:md5,60073848cd4fac905fe5c3a2cacb0dde",
+                        "cddannot_generic.dat:md5,7b1f2e6149469f394b7688cb8685d111",
+                        "cddid.tbl:md5,51831ce178d98aeb2b9b3cdebe9069fe",
+                        "cdtrack.txt:md5,dc94bb9a8e8027d40a344d78828c2661",
+                        "family_superfamily_links:md5,456e18a5310f1abd48521c11616b04d1"
+                    ]
+                ]
+            ],
+            {
+                "versions_tar": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "untar",
+                        "1.32.1"
+                    ]
+                ],
+                "versions_wget": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "wget",
+                        "1.18"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-17T15:17:48.242008"
+    },
+    "cdddownload - smart - stub": {
+        "content": [
+            [
+                [
+                    
+                ]
+            ],
+            {
+                "versions_tar": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "untar",
+                        "1.32.1"
+                    ]
+                ],
+                "versions_wget": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "wget",
+                        "1.18"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-17T15:17:56.733196"
+    },
+    "cdddownload - smart": {
+        "content": [
+            [
+                [
+                    [
+                        "Smart.aux:md5,4676e5073e915b31726844ed20a768d2",
+                        "Smart.freq:md5,2fa7da70eb0697574ab484d625493b46",
+                        "Smart.loo:md5,c17ab45e4e8e7316adc9148d39e40f4b",
+                        "Smart.pdb:md5,fb463e0703f2bd9b75068b1f0eb71a5d",
+                        "Smart.phr:md5,acb5655696f6948baf7ba8064f7adb58",
+                        "Smart.pin:md5,af1c29799b5c5168481bceb3c6d8cdd8",
+                        "Smart.pos:md5,4a1c4bc186ba31897ac53ecaa2749cdf",
+                        "Smart.pot:md5,8954644983f3cf5d0d24cbcc1a531a21",
+                        "Smart.psq:md5,ca89b28ce23aa7e7246359293ec0a480",
+                        "Smart.ptf:md5,36ec33f1546d8065dce4d7d646b9d707",
+                        "Smart.pto:md5,9a94d5d06ba316923905c46eb30c76bc",
+                        "Smart.rps:md5,fc24261c5717fc4b4696516a330eba5e"
+                    ],
+                    [
+                        "bitscore_specific.txt:md5,417ab1c1223f42a38cb4c0caee8165f5",
+                        "cddannot.dat:md5,60073848cd4fac905fe5c3a2cacb0dde",
+                        "cddannot_generic.dat:md5,7b1f2e6149469f394b7688cb8685d111",
+                        "cddid.tbl:md5,51831ce178d98aeb2b9b3cdebe9069fe",
+                        "cdtrack.txt:md5,dc94bb9a8e8027d40a344d78828c2661",
+                        "family_superfamily_links:md5,456e18a5310f1abd48521c11616b04d1"
+                    ]
+                ]
+            ],
+            {
+                "versions_tar": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "untar",
+                        "1.32.1"
+                    ]
+                ],
+                "versions_wget": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "wget",
+                        "1.18"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-17T15:16:28.523365"
+    },
+    "cdddownload - default Cdd_NCBI - stub": {
+        "content": [
+            [
+                [
+                    
+                ]
+            ],
+            {
+                "versions_tar": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "untar",
+                        "1.32.1"
+                    ]
+                ],
+                "versions_wget": [
+                    [
+                        "BLAST_CDDDOWNLOADER",
+                        "wget",
+                        "1.18"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-17T15:18:04.848933"
+    }
+}
\ No newline at end of file

From 136d5213d1bc02d45323c4dfae743d9d7ad0e1a4 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Wed, 17 Dec 2025 16:00:53 +0000
Subject: [PATCH 02/15] Fix lint

---
 modules/nf-core/blast/cdddownloader/meta.yml | 24 ++++++++------------
 1 file changed, 9 insertions(+), 15 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/meta.yml b/modules/nf-core/blast/cdddownloader/meta.yml
index ef9070d0adac..a004e004afb7 100644
--- a/modules/nf-core/blast/cdddownloader/meta.yml
+++ b/modules/nf-core/blast/cdddownloader/meta.yml
@@ -30,28 +30,28 @@ input:
       pattern: "Cdd|Cdd_NCBI|Cog|Kog|Pfam|Prk|Smart|Tigr"
 output:
   db:
-    - cdd_databases:
+    - cdd_databases/:
         type: directory
-        description: Directory containing the CDD database
-        pattern: "cdd_databases"
+        description: Directory containing the CDD database files
+        pattern: "cdd_databases/"
   versions_wget:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "wget":
+      - wget:
           type: string
           description: The name of the tool
-      - "wget --version | head -1 | cut -d ' ' -f 3":
+      - wget --version | head -1 | cut -d ' ' -f 3:
           type: eval
           description: The expression to obtain the version of the tool
   versions_tar:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "untar":
+      - untar:
           type: string
           description: The name of the tool
-      - "tar --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -1":
+      - 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:
@@ -65,12 +65,6 @@ topics:
       - wget --version | head -1 | cut -d ' ' -f 3:
           type: eval
           description: The expression to obtain the version of the tool
-      - tar:
-          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
 authors:
   - "@Ales-ibt"
 maintainers:

From b256e2168cfcdc22899d29d05278d9833ce1f8cb Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Wed, 17 Dec 2025 16:12:10 +0000
Subject: [PATCH 03/15] fix lint

---
 modules/nf-core/blast/cdddownloader/meta.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/modules/nf-core/blast/cdddownloader/meta.yml b/modules/nf-core/blast/cdddownloader/meta.yml
index a004e004afb7..9162b47b7d3a 100644
--- a/modules/nf-core/blast/cdddownloader/meta.yml
+++ b/modules/nf-core/blast/cdddownloader/meta.yml
@@ -65,6 +65,12 @@ topics:
       - wget --version | head -1 | cut -d ' ' -f 3:
           type: eval
           description: The expression to obtain the version of the tool
+      - 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
 authors:
   - "@Ales-ibt"
 maintainers:

From c534914660e1fe1c282957250d707528249cfeb8 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 18 Dec 2025 12:58:00 +0000
Subject: [PATCH 04/15] Adding handlers for existing db dirs

---
 modules/nf-core/blast/cdddownloader/main.nf   | 72 ++++++++++++++-----
 modules/nf-core/blast/cdddownloader/meta.yml  | 28 ++++----
 .../blast/cdddownloader/tests/main.nf.test    | 11 ++-
 .../cdddownloader/tests/main.nf.test.snap     | 12 ++--
 4 files changed, 81 insertions(+), 42 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/main.nf b/modules/nf-core/blast/cdddownloader/main.nf
index 1059458dd027..55175d89fc30 100644
--- a/modules/nf-core/blast/cdddownloader/main.nf
+++ b/modules/nf-core/blast/cdddownloader/main.nf
@@ -9,9 +9,10 @@ process BLAST_CDDDOWNLOADER {
 
     input:
     val db_prefix
+    path download_path
 
     output:
-    path "cdd_databases/", emit: db
+    path "${download_path}/cdd_databases/", emit: db
     tuple val("${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
 
@@ -40,24 +41,63 @@ process BLAST_CDDDOWNLOADER {
     }
 
     """
-    mkdir -p cdd_databases/${db_prefix}
-    cd cdd_databases/
-    mkdir data
+    # Check if cdd_databases directory exists in download_path
+    if [ -d "${download_path}/cdd_databases" ]; then
+        echo "Found existing cdd_databases directory at ${download_path}"
+        cd ${download_path}/cdd_databases
 
-    echo "Downloading ${db_prefix} database into ${db_prefix} dir"
+        # Check if db_prefix directory exists
+        if [ -d "${db_prefix}" ]; then
+            file_count=\$(find ${db_prefix} -type f | wc -l)
+            echo "WARNING: The directory ${download_path}/cdd_databases/${db_prefix} already exists and contains \${file_count} files."
+            echo "If you want to download the database ${db_prefix} again, remove the current ${db_prefix} directory first."
+        else
+            echo "Creating ${db_prefix} directory and downloading database..."
+            mkdir ${db_prefix}
+            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 "Database ${db_prefix} downloaded successfully"
+        fi
 
-    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
+        # Check if data directory exists
+        if [ -d "data" ]; then
+            data_file_count=\$(find data -type f | wc -l)
+            echo "The directory ${download_path}/cdd_databases/data already exists and contains \${data_file_count} files."
+            echo "Skipping metadata files downloading"
+            echo "If you want to download the metadata files again, remove the current data directory first."
+        else
+            echo "Creating data directory and downloading metadata files..."
+            mkdir data
+            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 "Metadata files downloaded successfully"
+        fi
+    else
+        echo "Creating new cdd_databases directory structure at ${download_path}"
+        mkdir -p ${download_path}/cdd_databases/${db_prefix}
+        mkdir -p ${download_path}/cdd_databases/data
+        cd ${download_path}/cdd_databases
 
-    echo "Downloading metadata files"
+        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
 
-    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 "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
+    fi
 
     echo "Finish"
 
@@ -65,6 +105,6 @@ process BLAST_CDDDOWNLOADER {
 
     stub:
     """
-    mkdir cdd_databases/
+    mkdir output/cdd_databases/
     """
 }
diff --git a/modules/nf-core/blast/cdddownloader/meta.yml b/modules/nf-core/blast/cdddownloader/meta.yml
index 9162b47b7d3a..3281b666780d 100644
--- a/modules/nf-core/blast/cdddownloader/meta.yml
+++ b/modules/nf-core/blast/cdddownloader/meta.yml
@@ -9,18 +9,13 @@ keywords:
   - 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:
+  - blast:
       description: |
-        Extract tar, tar.gz, tar.bz2, tar.xz files.
-      documentation: https://www.gnu.org/software/tar/manual/
-      licence: ["GPL-3.0-or-later"]
+        BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.
+      homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
+      documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
+      doi: 10.1016/S0022-2836(05)80360-2
+      licence: ["US-Government-Work"]
       identifier: ""
 input:
   - db_prefix:
@@ -28,12 +23,19 @@ input:
       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"
+  - download_path:
+      type: directory
+      description: |
+        The path where the databases should be downloaded
+      pattern: "*/"
 output:
   db:
     - cdd_databases/:
         type: directory
-        description: Directory containing the CDD database files
-        pattern: "cdd_databases/"
+        description: |
+          Directory containing the CDD database files, located at download_path/cdd_databases.
+          Contains subdirectories for the specified database prefix and a 'data' directory with metadata files.
+        pattern: "*/cdd_databases/"
   versions_wget:
     - - ${task.process}:
           type: string
diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test b/modules/nf-core/blast/cdddownloader/tests/main.nf.test
index 0b501cbaa417..0db52a91126c 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test
@@ -14,10 +14,10 @@ nextflow_process {
             process {
                 """
                 input[0] = 'Smart'
+                input[1] = file("${outputDir}")
                 """
             }
         }
-
         then {
             assert process.success
             assertAll(
@@ -27,7 +27,6 @@ nextflow_process {
                 ).match() }
             )
         }
-
     }
 
     test("cdddownload - default Cdd_NCBI") {
@@ -35,10 +34,10 @@ nextflow_process {
             process {
                 """
                 input[0] = ''
+                input[1] = file("${outputDir}")
                 """
             }
         }
-
         then {
             assert process.success
             assertAll(
@@ -48,7 +47,6 @@ nextflow_process {
                 ).match() }
             )
         }
-
     }
 
     test("cdddownload - smart - stub") {
@@ -59,10 +57,10 @@ nextflow_process {
             process {
                 """
                 input[0] = 'Smart'
+                input[1] = file("${outputDir}")
                 """
             }
         }
-
         then {
             assert process.success
             assertAll(
@@ -83,10 +81,10 @@ nextflow_process {
             process {
                 """
                 input[0] = ''
+                input[1] = file("${outputDir}")
                 """
             }
         }
-
         then {
             assert process.success
             assertAll(
@@ -96,7 +94,6 @@ nextflow_process {
                 ).match() }
             )
         }
-
     }
 
 }
diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
index 3918fcf93af4..c073e8064ac6 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -108,7 +108,7 @@
                         "cddannot_generic.dat:md5,7b1f2e6149469f394b7688cb8685d111",
                         "cddid.tbl:md5,51831ce178d98aeb2b9b3cdebe9069fe",
                         "cdtrack.txt:md5,dc94bb9a8e8027d40a344d78828c2661",
-                        "family_superfamily_links:md5,456e18a5310f1abd48521c11616b04d1"
+                        "family_superfamily_links:md5,3af9f63b6aa9ab822666c77059fe9c08"
                     ]
                 ]
             ],
@@ -133,7 +133,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-17T15:17:48.242008"
+        "timestamp": "2025-12-18T12:46:20.087856"
     },
     "cdddownload - smart - stub": {
         "content": [
@@ -163,7 +163,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-17T15:17:56.733196"
+        "timestamp": "2025-12-18T12:46:28.501523"
     },
     "cdddownload - smart": {
         "content": [
@@ -189,7 +189,7 @@
                         "cddannot_generic.dat:md5,7b1f2e6149469f394b7688cb8685d111",
                         "cddid.tbl:md5,51831ce178d98aeb2b9b3cdebe9069fe",
                         "cdtrack.txt:md5,dc94bb9a8e8027d40a344d78828c2661",
-                        "family_superfamily_links:md5,456e18a5310f1abd48521c11616b04d1"
+                        "family_superfamily_links:md5,3af9f63b6aa9ab822666c77059fe9c08"
                     ]
                 ]
             ],
@@ -214,7 +214,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-17T15:16:28.523365"
+        "timestamp": "2025-12-18T12:44:22.847117"
     },
     "cdddownload - default Cdd_NCBI - stub": {
         "content": [
@@ -244,6 +244,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-17T15:18:04.848933"
+        "timestamp": "2025-12-18T12:46:36.422213"
     }
 }
\ No newline at end of file

From b4f72abf19410668e55a96bc9899840f25031b53 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 18 Dec 2025 13:10:01 +0000
Subject: [PATCH 05/15] Fixing output path

---
 modules/nf-core/blast/cdddownloader/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/blast/cdddownloader/meta.yml b/modules/nf-core/blast/cdddownloader/meta.yml
index 3281b666780d..6e76377e53a6 100644
--- a/modules/nf-core/blast/cdddownloader/meta.yml
+++ b/modules/nf-core/blast/cdddownloader/meta.yml
@@ -30,7 +30,7 @@ input:
       pattern: "*/"
 output:
   db:
-    - cdd_databases/:
+    - ${download_path}/cdd_databases/:
         type: directory
         description: |
           Directory containing the CDD database files, located at download_path/cdd_databases.

From 2a782abfeb48a882f3e21f770811d68ba9f7f0a1 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 18 Dec 2025 13:17:58 +0000
Subject: [PATCH 06/15] Fixing output path

---
 .../nf-core/blast/cdddownloader/tests/main.nf.test.snap   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
index c073e8064ac6..e64194ecb609 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -133,7 +133,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T12:46:20.087856"
+        "timestamp": "2025-12-18T13:12:43.946878"
     },
     "cdddownload - smart - stub": {
         "content": [
@@ -163,7 +163,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T12:46:28.501523"
+        "timestamp": "2025-12-18T13:12:52.346936"
     },
     "cdddownload - smart": {
         "content": [
@@ -214,7 +214,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T12:44:22.847117"
+        "timestamp": "2025-12-18T13:10:52.603498"
     },
     "cdddownload - default Cdd_NCBI - stub": {
         "content": [
@@ -244,6 +244,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T12:46:36.422213"
+        "timestamp": "2025-12-18T13:13:00.386649"
     }
 }
\ No newline at end of file

From 73bbc7d15e8a292a4e161bed2c8b507dcbee2716 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 18 Dec 2025 13:36:31 +0000
Subject: [PATCH 07/15] Fixing meta.yml with nf-core tools v3.6.0.dev0

---
 modules/nf-core/blast/cdddownloader/meta.yml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/meta.yml b/modules/nf-core/blast/cdddownloader/meta.yml
index 6e76377e53a6..54b72eb4832e 100644
--- a/modules/nf-core/blast/cdddownloader/meta.yml
+++ b/modules/nf-core/blast/cdddownloader/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "blast_cdddownloader"
 description: CDD databases downloader
 keywords:
@@ -53,9 +52,10 @@ output:
       - untar:
           type: string
           description: The name of the tool
-      - tar --version 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+' | head -1:
+      - 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}:
@@ -67,12 +67,16 @@ topics:
       - wget --version | head -1 | cut -d ' ' -f 3:
           type: eval
           description: The expression to obtain the version of the tool
+    - - ${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:
+      - 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
+
 authors:
   - "@Ales-ibt"
 maintainers:

From 85d2c72e569d4d39f2e96c7cd4e2e6aa754df9d9 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 18 Dec 2025 13:49:14 +0000
Subject: [PATCH 08/15] updating snap

---
 .../nf-core/blast/cdddownloader/tests/main.nf.test.snap   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
index e64194ecb609..56e9f151fb00 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -133,7 +133,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:12:43.946878"
+        "timestamp": "2025-12-18T13:43:54.288357"
     },
     "cdddownload - smart - stub": {
         "content": [
@@ -163,7 +163,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:12:52.346936"
+        "timestamp": "2025-12-18T13:44:02.657114"
     },
     "cdddownload - smart": {
         "content": [
@@ -214,7 +214,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:10:52.603498"
+        "timestamp": "2025-12-18T13:42:02.951994"
     },
     "cdddownload - default Cdd_NCBI - stub": {
         "content": [
@@ -244,6 +244,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:13:00.386649"
+        "timestamp": "2025-12-18T13:44:10.721201"
     }
 }
\ No newline at end of file

From 7f422dd712495ea520b448984c8c8b48ead047df Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 18 Dec 2025 13:59:07 +0000
Subject: [PATCH 09/15] Adding tar to env

---
 modules/nf-core/blast/cdddownloader/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/blast/cdddownloader/environment.yml b/modules/nf-core/blast/cdddownloader/environment.yml
index 2a5094dc4823..1eb2256f44b2 100644
--- a/modules/nf-core/blast/cdddownloader/environment.yml
+++ b/modules/nf-core/blast/cdddownloader/environment.yml
@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::gnu-wget=1.18
+  - conda-forge::tar=1.34

From c783146780706fa7b910261b8d94dbaa292b20cc Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Fri, 19 Dec 2025 09:03:13 +0000
Subject: [PATCH 10/15] snap updated

---
 .../cdddownloader/tests/main.nf.test.snap     | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
index 56e9f151fb00..793dae7d481b 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -117,14 +117,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "1.32.1"
+                        "3.5.3"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.18"
+                        "1.25.0"
                     ]
                 ]
             }
@@ -133,7 +133,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:43:54.288357"
+        "timestamp": "2025-12-19T08:59:03.602489"
     },
     "cdddownload - smart - stub": {
         "content": [
@@ -147,14 +147,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "1.32.1"
+                        "3.5.3"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.18"
+                        "1.25.0"
                     ]
                 ]
             }
@@ -163,7 +163,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:44:02.657114"
+        "timestamp": "2025-12-19T08:59:10.533945"
     },
     "cdddownload - smart": {
         "content": [
@@ -198,14 +198,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "1.32.1"
+                        "3.5.3"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.18"
+                        "1.25.0"
                     ]
                 ]
             }
@@ -214,7 +214,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:42:02.951994"
+        "timestamp": "2025-12-19T08:57:42.186661"
     },
     "cdddownload - default Cdd_NCBI - stub": {
         "content": [
@@ -228,14 +228,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "1.32.1"
+                        "3.5.3"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.18"
+                        "1.25.0"
                     ]
                 ]
             }
@@ -244,6 +244,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-18T13:44:10.721201"
+        "timestamp": "2025-12-19T08:59:17.348407"
     }
 }
\ No newline at end of file

From b99941477374d6d168a291d0f0ce9b557d5b7507 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Fri, 19 Dec 2025 09:13:51 +0000
Subject: [PATCH 11/15] Updating conda versions

---
 .../blast/cdddownloader/environment.yml       |  2 +-
 .../cdddownloader/tests/main.nf.test.snap     | 24 +++++++++----------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/environment.yml b/modules/nf-core/blast/cdddownloader/environment.yml
index 1eb2256f44b2..067f3714ed89 100644
--- a/modules/nf-core/blast/cdddownloader/environment.yml
+++ b/modules/nf-core/blast/cdddownloader/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::gnu-wget=1.18
-  - conda-forge::tar=1.34
+  - conda-forge::tar=1.32.1
diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
index 793dae7d481b..d2d33bf4affb 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -117,14 +117,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "3.5.3"
+                        "1.32.1"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.25.0"
+                        "1.18"
                     ]
                 ]
             }
@@ -133,7 +133,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T08:59:03.602489"
+        "timestamp": "2025-12-19T09:10:59.657345"
     },
     "cdddownload - smart - stub": {
         "content": [
@@ -147,14 +147,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "3.5.3"
+                        "1.32.1"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.25.0"
+                        "1.18"
                     ]
                 ]
             }
@@ -163,7 +163,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T08:59:10.533945"
+        "timestamp": "2025-12-19T09:11:08.711033"
     },
     "cdddownload - smart": {
         "content": [
@@ -198,14 +198,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "3.5.3"
+                        "1.32.1"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.25.0"
+                        "1.18"
                     ]
                 ]
             }
@@ -214,7 +214,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T08:57:42.186661"
+        "timestamp": "2025-12-19T09:09:09.212084"
     },
     "cdddownload - default Cdd_NCBI - stub": {
         "content": [
@@ -228,14 +228,14 @@
                     [
                         "BLAST_CDDDOWNLOADER",
                         "untar",
-                        "3.5.3"
+                        "1.32.1"
                     ]
                 ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
                         "wget",
-                        "1.25.0"
+                        "1.18"
                     ]
                 ]
             }
@@ -244,6 +244,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T08:59:17.348407"
+        "timestamp": "2025-12-19T09:11:16.837679"
     }
 }
\ No newline at end of file

From 2f5d0a7f05773fe66d359c03943cb30d8b6e4f66 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Fri, 19 Dec 2025 09:24:14 +0000
Subject: [PATCH 12/15] Updating tar version

---
 modules/nf-core/blast/cdddownloader/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/blast/cdddownloader/environment.yml b/modules/nf-core/blast/cdddownloader/environment.yml
index 067f3714ed89..345d5b47c785 100644
--- a/modules/nf-core/blast/cdddownloader/environment.yml
+++ b/modules/nf-core/blast/cdddownloader/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::gnu-wget=1.18
-  - conda-forge::tar=1.32.1
+  - conda-forge::tar=1.32

From a3f6f22cb5164d06f07ebeaefecd5a40e8138c58 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Fri, 19 Dec 2025 09:26:11 +0000
Subject: [PATCH 13/15] Updating tar version

---
 modules/nf-core/blast/cdddownloader/environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/blast/cdddownloader/environment.yml b/modules/nf-core/blast/cdddownloader/environment.yml
index 345d5b47c785..2a5094dc4823 100644
--- a/modules/nf-core/blast/cdddownloader/environment.yml
+++ b/modules/nf-core/blast/cdddownloader/environment.yml
@@ -5,4 +5,3 @@ channels:
   - bioconda
 dependencies:
   - bioconda::gnu-wget=1.18
-  - conda-forge::tar=1.32

From 463a2619aa93832547874f49ae52e0540ecee3a3 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Fri, 19 Dec 2025 09:29:32 +0000
Subject: [PATCH 14/15] Updating tar version

---
 modules/nf-core/blast/cdddownloader/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/blast/cdddownloader/environment.yml b/modules/nf-core/blast/cdddownloader/environment.yml
index 2a5094dc4823..345d5b47c785 100644
--- a/modules/nf-core/blast/cdddownloader/environment.yml
+++ b/modules/nf-core/blast/cdddownloader/environment.yml
@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::gnu-wget=1.18
+  - conda-forge::tar=1.32

From 1fe1cc7c5b4ec689f047b7093b1e9cd8d71a14d6 Mon Sep 17 00:00:00 2001
From: Ales-ibt <ales@ebi.ac.uk>
Date: Thu, 8 Jan 2026 10:04:23 +0000
Subject: [PATCH 15/15] Removing tar from snap

---
 .../blast/cdddownloader/tests/main.nf.test    |  9 +++--
 .../cdddownloader/tests/main.nf.test.snap     | 36 +++----------------
 2 files changed, 8 insertions(+), 37 deletions(-)

diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test b/modules/nf-core/blast/cdddownloader/tests/main.nf.test
index 0db52a91126c..ff608411e85e 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out.db,
-                    process.out.findAll { key, val -> key.startsWith("versions")}
+                    process.out.findAll { key, val -> key.startsWith("versions") && !key.contains("tar")}
                 ).match() }
             )
         }
@@ -43,7 +43,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out.db,
-                    process.out.findAll { key, val -> key.startsWith("versions")}
+                    process.out.findAll { key, val -> key.startsWith("versions") && !key.contains("tar")}
                 ).match() }
             )
         }
@@ -66,7 +66,7 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out.db,
-                    process.out.findAll { key, val -> key.startsWith("versions")}
+                    process.out.findAll { key, val -> key.startsWith("versions") && !key.contains("tar")}
                 ).match() }
             )
         }
@@ -90,10 +90,9 @@ nextflow_process {
             assertAll(
                 { assert snapshot(
                     process.out.db,
-                    process.out.findAll { key, val -> key.startsWith("versions")}
+                    process.out.findAll { key, val -> key.startsWith("versions") && !key.contains("tar")}
                 ).match() }
             )
         }
     }
-
 }
diff --git a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
index d2d33bf4affb..d5b1d8a20c23 100644
--- a/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/cdddownloader/tests/main.nf.test.snap
@@ -113,13 +113,6 @@
                 ]
             ],
             {
-                "versions_tar": [
-                    [
-                        "BLAST_CDDDOWNLOADER",
-                        "untar",
-                        "1.32.1"
-                    ]
-                ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
@@ -133,7 +126,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T09:10:59.657345"
+        "timestamp": "2026-01-08T10:00:36.017382"
     },
     "cdddownload - smart - stub": {
         "content": [
@@ -143,13 +136,6 @@
                 ]
             ],
             {
-                "versions_tar": [
-                    [
-                        "BLAST_CDDDOWNLOADER",
-                        "untar",
-                        "1.32.1"
-                    ]
-                ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
@@ -163,7 +149,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T09:11:08.711033"
+        "timestamp": "2026-01-08T10:00:44.61215"
     },
     "cdddownload - smart": {
         "content": [
@@ -194,13 +180,6 @@
                 ]
             ],
             {
-                "versions_tar": [
-                    [
-                        "BLAST_CDDDOWNLOADER",
-                        "untar",
-                        "1.32.1"
-                    ]
-                ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
@@ -214,7 +193,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T09:09:09.212084"
+        "timestamp": "2026-01-08T09:58:45.551095"
     },
     "cdddownload - default Cdd_NCBI - stub": {
         "content": [
@@ -224,13 +203,6 @@
                 ]
             ],
             {
-                "versions_tar": [
-                    [
-                        "BLAST_CDDDOWNLOADER",
-                        "untar",
-                        "1.32.1"
-                    ]
-                ],
                 "versions_wget": [
                     [
                         "BLAST_CDDDOWNLOADER",
@@ -244,6 +216,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-12-19T09:11:16.837679"
+        "timestamp": "2026-01-08T10:00:52.717569"
     }
 }
\ No newline at end of file