From c9c80529892cb28a42e5bfc76bf6d9aa37b8cd66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 12:44:55 +0200
Subject: [PATCH 01/16] add crabs/dbimport from readsimulator pipeline

---
 .../nf-core/crabs/dbimport/environment.yml    |  7 ++
 modules/nf-core/crabs/dbimport/main.nf        | 56 +++++++++++++++
 modules/nf-core/crabs/dbimport/meta.yml       | 49 +++++++++++++
 .../nf-core/crabs/dbimport/tests/main.nf.test | 59 ++++++++++++++++
 .../crabs/dbimport/tests/main.nf.test.snap    | 68 +++++++++++++++++++
 .../crabs/dbimport/tests/nextflow.config      |  7 ++
 modules/nf-core/crabs/dbimport/tests/tags.yml |  2 +
 7 files changed, 248 insertions(+)
 create mode 100644 modules/nf-core/crabs/dbimport/environment.yml
 create mode 100644 modules/nf-core/crabs/dbimport/main.nf
 create mode 100644 modules/nf-core/crabs/dbimport/meta.yml
 create mode 100644 modules/nf-core/crabs/dbimport/tests/main.nf.test
 create mode 100644 modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/crabs/dbimport/tests/nextflow.config
 create mode 100644 modules/nf-core/crabs/dbimport/tests/tags.yml

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
new file mode 100644
index 00000000000..78fa255d3d9
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -0,0 +1,7 @@
+name: crabs_dbimport
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::crabs=0.1.1"
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
new file mode 100644
index 00000000000..4696fbab3e9
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/main.nf
@@ -0,0 +1,56 @@
+process CRABS_DBIMPORT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
+        'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.fa"), emit: fasta
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args          = task.ext.args ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
+    def VERSION       = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def is_compressed = fasta.name.endsWith(".gz")
+    def fasta_name    = fasta.name.replace(".gz", "")
+    """
+    if [ "${is_compressed}" == "true" ]; then
+        gzip -c -d ${fasta} > ${fasta_name}
+    fi
+
+    crabs db_import \\
+        --input ${fasta_name} \\
+        --output ${prefix}.crabsdb.fa \\
+        $args
+
+    rm ${fasta_name}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabs: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION       = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabs: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/crabs/dbimport/meta.yml b/modules/nf-core/crabs/dbimport/meta.yml
new file mode 100644
index 00000000000..030a450a260
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/meta.yml
@@ -0,0 +1,49 @@
+name: crabs_dbimport
+description: In-house generated or curated data can be imported into CRABS.
+keywords:
+  - insilico
+  - PCR
+tools:
+  - crabs:
+      description: |
+        Crabs (Creating Reference databases for Amplicon-Based Sequencing)
+        is a program to download and curate reference databases
+        for eDNA metabarcoding analyses
+      homepage: https://github.com/gjeunen/reference_database_creator
+      documentation: https://github.com/gjeunen/reference_database_creator?tab=readme-ov-file#running-crabs
+      tool_dev_url: https://github.com/gjeunen/reference_database_creator
+      doi: https://doi.org/10.1111/1755-0998.13741
+      licence: ["MIT License"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fasta:
+      type: file
+      description: In-house sequencing data
+      pattern: "*.{fa,fasta}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - fasta:
+      type: file
+      description: Reverse complemented Sequence
+      pattern: "*.{fa,fasta}"
+
+authors:
+  - "@famosab"
+  - "@a4000"
+maintainers:
+  - "@famosab"
+  - "@a4000"
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test b/modules/nf-core/crabs/dbimport/tests/main.nf.test
new file mode 100644
index 00000000000..c5ef876f05e
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test
@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process CRABS_DBIMPORT"
+    script "../main.nf"
+    process "CRABS_DBIMPORT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "crabs"
+    tag "crabs/dbimport"
+
+    test("sarscov2 - 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 - 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() }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
new file mode 100644
index 00000000000..e01938f9fef
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T12:42:46.076137"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.crabsdb.fa:md5,f46e9d5dbadcfda9a8d7d01e4bf7dfb2"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.crabsdb.fa:md5,f46e9d5dbadcfda9a8d7d01e4bf7dfb2"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T12:42:41.421262"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/crabs/dbimport/tests/nextflow.config b/modules/nf-core/crabs/dbimport/tests/nextflow.config
new file mode 100644
index 00000000000..282a7b2ebbd
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: CRABS_DBIMPORT {
+        ext.args = "--seq_header species --delim ' '"
+    }
+
+}
diff --git a/modules/nf-core/crabs/dbimport/tests/tags.yml b/modules/nf-core/crabs/dbimport/tests/tags.yml
new file mode 100644
index 00000000000..6efca4ca891
--- /dev/null
+++ b/modules/nf-core/crabs/dbimport/tests/tags.yml
@@ -0,0 +1,2 @@
+crabs/dbimport:
+  - "modules/nf-core/crabs/dbimport/**"

From 75e23c7a00dbab51f364e580fc1a965174596109 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 14:49:04 +0200
Subject: [PATCH 02/16] fix linting

---
 modules/nf-core/crabs/dbimport/meta.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/crabs/dbimport/meta.yml b/modules/nf-core/crabs/dbimport/meta.yml
index 030a450a260..27424a0464b 100644
--- a/modules/nf-core/crabs/dbimport/meta.yml
+++ b/modules/nf-core/crabs/dbimport/meta.yml
@@ -2,7 +2,9 @@ name: crabs_dbimport
 description: In-house generated or curated data can be imported into CRABS.
 keywords:
   - insilico
-  - PCR
+  - amplicon
+  - sequencing
+  - inhouse
 tools:
   - crabs:
       description: |

From a971dd7dd9d9d99c5c795f1ed6b1b5839add9faa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 14:54:53 +0200
Subject: [PATCH 03/16] remove defaults

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

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 78fa255d3d9..b81fb837b14 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -2,6 +2,5 @@ name: crabs_dbimport
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::crabs=0.1.1"

From 4306c6ccae64301757debb3bf308fa5177d9ba41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 15:26:00 +0200
Subject: [PATCH 04/16] update crabs with wave containers

---
 modules/nf-core/crabs/dbimport/environment.yml       |  7 ++++++-
 modules/nf-core/crabs/dbimport/main.nf               | 11 ++++-------
 .../nf-core/crabs/dbimport/tests/main.nf.test.snap   | 12 ++++++------
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index b81fb837b14..9a872a4af05 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -3,4 +3,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::crabs=0.1.1"
+  - wget=1.21.3
+  - muscle=3.8.31
+  - cutadapt>=4.0
+  - vsearch>=2.13.3
+  - pip:
+      - crabs==0.2
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
index 4696fbab3e9..a73339cb30b 100644
--- a/modules/nf-core/crabs/dbimport/main.nf
+++ b/modules/nf-core/crabs/dbimport/main.nf
@@ -2,11 +2,10 @@ process CRABS_DBIMPORT {
     tag "$meta.id"
     label 'process_medium'
 
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
-        'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"
+        'oras://community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:0cd5cb1e549e5033':
+        'community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:04f6c0370c0226c5' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -21,7 +20,6 @@ process CRABS_DBIMPORT {
     script:
     def args          = task.ext.args ?: ''
     def prefix        = task.ext.prefix ?: "${meta.id}"
-    def VERSION       = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     def is_compressed = fasta.name.endsWith(".gz")
     def fasta_name    = fasta.name.replace(".gz", "")
     """
@@ -38,19 +36,18 @@ process CRABS_DBIMPORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        crabs: $VERSION
+        crabs: \$(crabs --version | sed -e 's/crabs v//g')
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION       = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        crabs: $VERSION
+        crabs: \$(crabs --version | sed -e 's/crabs v//g')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
index e01938f9fef..a237dcd51b7 100644
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ],
                 "fasta": [
                     [
@@ -22,7 +22,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ]
             }
         ],
@@ -30,7 +30,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T12:42:46.076137"
+        "timestamp": "2024-09-05T15:25:04.701271"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ],
                 "fasta": [
                     [
@@ -55,7 +55,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ]
             }
         ],
@@ -63,6 +63,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T12:42:41.421262"
+        "timestamp": "2024-09-05T15:24:57.657881"
     }
 }
\ No newline at end of file

From 75f141b7a005dc157c6a071de62bcc06be362c1c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 15:41:00 +0200
Subject: [PATCH 05/16] update meta

---
 modules/nf-core/crabs/dbimport/environment.yml | 1 +
 modules/nf-core/crabs/dbimport/meta.yml        | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 9a872a4af05..81f9937843e 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -7,5 +7,6 @@ dependencies:
   - muscle=3.8.31
   - cutadapt>=4.0
   - vsearch>=2.13.3
+  - pip>=23.2
   - pip:
       - crabs==0.2
diff --git a/modules/nf-core/crabs/dbimport/meta.yml b/modules/nf-core/crabs/dbimport/meta.yml
index 27424a0464b..e7ac1de3e70 100644
--- a/modules/nf-core/crabs/dbimport/meta.yml
+++ b/modules/nf-core/crabs/dbimport/meta.yml
@@ -14,7 +14,7 @@ tools:
       homepage: https://github.com/gjeunen/reference_database_creator
       documentation: https://github.com/gjeunen/reference_database_creator?tab=readme-ov-file#running-crabs
       tool_dev_url: https://github.com/gjeunen/reference_database_creator
-      doi: https://doi.org/10.1111/1755-0998.13741
+      doi: 10.1111/1755-0998.13741
       licence: ["MIT License"]
 
 input:

From d29bb4d87cef7813aa7983b85fa28f8da4bf08fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:06:15 +0200
Subject: [PATCH 06/16] remove name

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

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 81f9937843e..732638a8038 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -1,4 +1,3 @@
-name: crabs_dbimport
 channels:
   - conda-forge
   - bioconda

From 5f9a4f9d085a45ab7f25303efa8cf126b8c04874 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:34:38 +0200
Subject: [PATCH 07/16] update env

---
 modules/nf-core/crabs/dbimport/environment.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 732638a8038..489866b9e39 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -2,10 +2,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - wget=1.21.3
-  - muscle=3.8.31
-  - cutadapt>=4.0
-  - vsearch>=2.13.3
-  - pip>=23.2
+  - bioconda::cutadapt=4.9
+  - bioconda::muscle=3.8.31
+  - bioconda::vsearch=2.28.1
+  - conda-forge::wget=1.20.3
+  - pip
   - pip:
-      - crabs==0.2
+    - crabs==0.2.0

From bb36e93746033b7760f93674e08ae0635dba87ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:36:20 +0200
Subject: [PATCH 08/16] prettier

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

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 489866b9e39..5bbf98b7f43 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -8,4 +8,4 @@ dependencies:
   - conda-forge::wget=1.20.3
   - pip
   - pip:
-    - crabs==0.2.0
+      - crabs==0.2.0

From 084ab4d6ddc008689adcc3aff41fb846ccfe4974 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 10:03:34 +0200
Subject: [PATCH 09/16] fix pip version

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

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 5bbf98b7f43..ceed5f98e28 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -6,6 +6,6 @@ dependencies:
   - bioconda::muscle=3.8.31
   - bioconda::vsearch=2.28.1
   - conda-forge::wget=1.20.3
-  - pip
+  - conda-forge::pip=24.2
   - pip:
       - crabs==0.2.0

From ad306317c5f6621a54795e3db2696388759f6e4c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 25 Oct 2024 13:04:48 +0200
Subject: [PATCH 10/16] update to 1.0.4 new structure needs resolving

---
 modules/nf-core/crabs/dbimport/environment.yml       | 8 +-------
 modules/nf-core/crabs/dbimport/main.nf               | 6 +++---
 modules/nf-core/crabs/dbimport/tests/nextflow.config | 2 +-
 3 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index ceed5f98e28..20be3a698d8 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -2,10 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::cutadapt=4.9
-  - bioconda::muscle=3.8.31
-  - bioconda::vsearch=2.28.1
-  - conda-forge::wget=1.20.3
-  - conda-forge::pip=24.2
-  - pip:
-      - crabs==0.2.0
+  - bioconda::crabs==1.0.4
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
index a73339cb30b..f715c222bcd 100644
--- a/modules/nf-core/crabs/dbimport/main.nf
+++ b/modules/nf-core/crabs/dbimport/main.nf
@@ -4,8 +4,8 @@ process CRABS_DBIMPORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:0cd5cb1e549e5033':
-        'community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:04f6c0370c0226c5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e0007b6b35c9783203b7fde287c383ac38168ecfee79639393e3cb1cd4afdaef/data':
+        'community.wave.seqera.io/library/crabs:1.0.4--1de4f5571e3e4ab0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -27,7 +27,7 @@ process CRABS_DBIMPORT {
         gzip -c -d ${fasta} > ${fasta_name}
     fi
 
-    crabs db_import \\
+    crabs --import \\
         --input ${fasta_name} \\
         --output ${prefix}.crabsdb.fa \\
         $args
diff --git a/modules/nf-core/crabs/dbimport/tests/nextflow.config b/modules/nf-core/crabs/dbimport/tests/nextflow.config
index 282a7b2ebbd..0a335183d8e 100644
--- a/modules/nf-core/crabs/dbimport/tests/nextflow.config
+++ b/modules/nf-core/crabs/dbimport/tests/nextflow.config
@@ -1,7 +1,7 @@
 process {
 
     withName: CRABS_DBIMPORT {
-        ext.args = "--seq_header species --delim ' '"
+        ext.args = "--seq_header species --delim ' ' --import-format embl \\"
     }
 
 }

From 5da0884bd2df5e7bba55337884ca6b97351afb47 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 18 Nov 2024 14:26:39 +0100
Subject: [PATCH 11/16] update

---
 .../nf-core/crabs/dbimport/environment.yml    |  2 +-
 modules/nf-core/crabs/dbimport/main.nf        |  4 +-
 modules/nf-core/crabs/dbimport/meta.yml       | 47 ++++++++++---------
 3 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 20be3a698d8..74ca9a2d9b3 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::crabs==1.0.4
+  - bioconda::crabs=1.0.6
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
index f715c222bcd..b8fdfbd2def 100644
--- a/modules/nf-core/crabs/dbimport/main.nf
+++ b/modules/nf-core/crabs/dbimport/main.nf
@@ -4,8 +4,8 @@ process CRABS_DBIMPORT {
 
     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/e0/e0007b6b35c9783203b7fde287c383ac38168ecfee79639393e3cb1cd4afdaef/data':
-        'community.wave.seqera.io/library/crabs:1.0.4--1de4f5571e3e4ab0' }"
+        'oras://community.wave.seqera.io/library/crabs:1.0.6--a95c7815a4a67eb2':
+        'community.wave.seqera.io/library/crabs:1.0.6--462aa28d85ee454e' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/crabs/dbimport/meta.yml b/modules/nf-core/crabs/dbimport/meta.yml
index e7ac1de3e70..0aeffde1558 100644
--- a/modules/nf-core/crabs/dbimport/meta.yml
+++ b/modules/nf-core/crabs/dbimport/meta.yml
@@ -16,33 +16,34 @@ tools:
       tool_dev_url: https://github.com/gjeunen/reference_database_creator
       doi: 10.1111/1755-0998.13741
       licence: ["MIT License"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1' ]`
-  - fasta:
-      type: file
-      description: In-house sequencing data
-      pattern: "*.{fa,fasta}"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: In-house sequencing data
+        pattern: "*.{fa,fasta}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1' ]`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - fasta:
-      type: file
-      description: Reverse complemented Sequence
-      pattern: "*.{fa,fasta}"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.fa":
+          type: file
+          description: Reverse complemented Sequence
+          pattern: "*.{fa,fasta}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@famosab"
   - "@a4000"

From 0af0158aafd0946e10222b865c6a3abb83e6714e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Wed, 20 Nov 2024 12:41:15 +0100
Subject: [PATCH 12/16] change ext args to new convention

---
 modules/nf-core/crabs/dbimport/tests/main.nf.test    | 3 +++
 modules/nf-core/crabs/dbimport/tests/nextflow.config | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test b/modules/nf-core/crabs/dbimport/tests/main.nf.test
index c5ef876f05e..17b30264335 100644
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test
@@ -13,6 +13,9 @@ nextflow_process {
     test("sarscov2 - fasta") {
 
         when {
+            params {
+                module_args = "--seq_header species --delim ' ' --import-format embl \\"
+            }
             process {
                 """
                 input[0] = [
diff --git a/modules/nf-core/crabs/dbimport/tests/nextflow.config b/modules/nf-core/crabs/dbimport/tests/nextflow.config
index 0a335183d8e..9d003f3db15 100644
--- a/modules/nf-core/crabs/dbimport/tests/nextflow.config
+++ b/modules/nf-core/crabs/dbimport/tests/nextflow.config
@@ -1,7 +1,7 @@
 process {
 
     withName: CRABS_DBIMPORT {
-        ext.args = "--seq_header species --delim ' ' --import-format embl \\"
+        ext.args = params.module_args
     }
 
 }

From 441d68d31525422e14c81ffef43b67738482601f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 12:57:01 +0900
Subject: [PATCH 13/16] remove tags and move config file

---
 modules/nf-core/crabs/dbimport/tests/main.nf.test | 3 ++-
 modules/nf-core/crabs/dbimport/tests/tags.yml     | 2 --
 2 files changed, 2 insertions(+), 3 deletions(-)
 delete mode 100644 modules/nf-core/crabs/dbimport/tests/tags.yml

diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test b/modules/nf-core/crabs/dbimport/tests/main.nf.test
index 17b30264335..6473abb1cbc 100644
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process CRABS_DBIMPORT"
     script "../main.nf"
     process "CRABS_DBIMPORT"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -12,6 +11,8 @@ nextflow_process {
 
     test("sarscov2 - fasta") {
 
+        config "./nextflow.config"
+
         when {
             params {
                 module_args = "--seq_header species --delim ' ' --import-format embl \\"
diff --git a/modules/nf-core/crabs/dbimport/tests/tags.yml b/modules/nf-core/crabs/dbimport/tests/tags.yml
deleted file mode 100644
index 6efca4ca891..00000000000
--- a/modules/nf-core/crabs/dbimport/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-crabs/dbimport:
-  - "modules/nf-core/crabs/dbimport/**"

From b35bb1adde14311a777044a92e8d4b43eed54639 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 14:22:11 +0900
Subject: [PATCH 14/16] add tests with download taxonomy

---
 .../nf-core/crabs/dbimport/environment.yml    |  2 +-
 modules/nf-core/crabs/dbimport/main.nf        | 14 +++++--
 .../nf-core/crabs/dbimport/tests/main.nf.test | 25 +++++++++++-
 .../crabs/dbimport/tests/main.nf.test.snap    | 39 ++++++++-----------
 4 files changed, 51 insertions(+), 29 deletions(-)

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
index 74ca9a2d9b3..c9761a2d14b 100644
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ b/modules/nf-core/crabs/dbimport/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::crabs=1.0.6
+  - bioconda::crabs=1.0.7
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
index b8fdfbd2def..ef00aea503f 100644
--- a/modules/nf-core/crabs/dbimport/main.nf
+++ b/modules/nf-core/crabs/dbimport/main.nf
@@ -4,11 +4,14 @@ process CRABS_DBIMPORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/crabs:1.0.6--a95c7815a4a67eb2':
-        'community.wave.seqera.io/library/crabs:1.0.6--462aa28d85ee454e' }"
+        'https://depot.galaxyproject.org/singularity/crabs:1.0.7--pyhdfd78af_0':
+        'biocontainers/crabs:1.0.7--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
+    tuple val(meta2), path(accession2taxid)
+    tuple val(meta3), path(names)
+    tuple val(meta4), path(nodes)
 
     output:
     tuple val(meta), path("*.fa"), emit: fasta
@@ -30,13 +33,16 @@ process CRABS_DBIMPORT {
     crabs --import \\
         --input ${fasta_name} \\
         --output ${prefix}.crabsdb.fa \\
+        --acc2tax ${accession2taxid} \\
+        --names ${names} \\
+        --nodes ${nodes} \\
         $args
 
     rm ${fasta_name}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        crabs: \$(crabs --version | sed -e 's/crabs v//g')
+        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
     END_VERSIONS
     """
 
@@ -47,7 +53,7 @@ process CRABS_DBIMPORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        crabs: \$(crabs --version | sed -e 's/crabs v//g')
+        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test b/modules/nf-core/crabs/dbimport/tests/main.nf.test
index 6473abb1cbc..b9f50699511 100644
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test
@@ -8,6 +8,18 @@ nextflow_process {
     tag "modules_nfcore"
     tag "crabs"
     tag "crabs/dbimport"
+    tag "crabs/downloadtaxonomy"
+
+    setup {
+        run("CRABS_DOWNLOADTAXONOMY") {
+            script "../../downloadtaxonomy/main.nf"
+            process {
+                """
+                input[0] = [ id:'taxonomy' ]
+                """
+            }
+        }
+    }
 
     test("sarscov2 - fasta") {
 
@@ -15,7 +27,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = "--seq_header species --delim ' ' --import-format embl \\"
+                module_args = "--import-format embl --ranks 'superkingdom;phylum;class;order;family;genus;species' \\"
             }
             process {
                 """
@@ -23,6 +35,9 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
+                input[1] = CRABS_DOWNLOADTAXONOMY.out.accession2taxid
+                input[2] = CRABS_DOWNLOADTAXONOMY.out.names
+                input[3] = CRABS_DOWNLOADTAXONOMY.out.nodes
                 """
             }
         }
@@ -47,6 +62,9 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
+                input[1] = CRABS_DOWNLOADTAXONOMY.out.accession2taxid
+                input[2] = CRABS_DOWNLOADTAXONOMY.out.names
+                input[3] = CRABS_DOWNLOADTAXONOMY.out.nodes
                 """
             }
         }
@@ -54,7 +72,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
             )
         }
 
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
index a237dcd51b7..54f52067cb6 100644
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
+++ b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
+                    "versions.yml:md5,65a68b87678624e13a185da907b3be67"
                 ],
                 "fasta": [
                     [
@@ -22,47 +22,42 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
+                    "versions.yml:md5,65a68b87678624e13a185da907b3be67"
                 ]
+            },
+            {
+                "CRABS_DBIMPORT": {
+                    "crabs": "v1.0.7"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-05T15:25:04.701271"
+        "timestamp": "2025-02-03T13:52:33.256766"
     },
     "sarscov2 - fasta": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.crabsdb.fa:md5,f46e9d5dbadcfda9a8d7d01e4bf7dfb2"
-                    ]
+                    
                 ],
                 "1": [
-                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
+                    
                 ],
                 "fasta": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.crabsdb.fa:md5,f46e9d5dbadcfda9a8d7d01e4bf7dfb2"
-                    ]
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
+                    
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-05T15:24:57.657881"
+        "timestamp": "2025-02-03T14:15:02.785883"
     }
 }
\ No newline at end of file

From a75fde14997171e65c9394607b601fce22e1ed50 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 14:30:00 +0900
Subject: [PATCH 15/16] add downloadtaxonomy module

---
 .../crabs/downloadtaxonomy/environment.yml    |   7 +
 .../nf-core/crabs/downloadtaxonomy/main.nf    |  53 +++++++
 .../nf-core/crabs/downloadtaxonomy/meta.yml   |  69 +++++++++
 .../crabs/downloadtaxonomy/tests/main.nf.test |  58 ++++++++
 .../downloadtaxonomy/tests/main.nf.test.snap  | 137 ++++++++++++++++++
 .../downloadtaxonomy/tests/nextflow.config    |   7 +
 6 files changed, 331 insertions(+)
 create mode 100644 modules/nf-core/crabs/downloadtaxonomy/environment.yml
 create mode 100644 modules/nf-core/crabs/downloadtaxonomy/main.nf
 create mode 100644 modules/nf-core/crabs/downloadtaxonomy/meta.yml
 create mode 100644 modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test
 create mode 100644 modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/crabs/downloadtaxonomy/tests/nextflow.config

diff --git a/modules/nf-core/crabs/downloadtaxonomy/environment.yml b/modules/nf-core/crabs/downloadtaxonomy/environment.yml
new file mode 100644
index 00000000000..79c320c88b9
--- /dev/null
+++ b/modules/nf-core/crabs/downloadtaxonomy/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::crabs=1.0.7"
diff --git a/modules/nf-core/crabs/downloadtaxonomy/main.nf b/modules/nf-core/crabs/downloadtaxonomy/main.nf
new file mode 100644
index 00000000000..bbf525726a2
--- /dev/null
+++ b/modules/nf-core/crabs/downloadtaxonomy/main.nf
@@ -0,0 +1,53 @@
+process CRABS_DOWNLOADTAXONOMY {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/crabs:1.0.7--pyhdfd78af_0':
+        'biocontainers/crabs:1.0.7--pyhdfd78af_0' }"
+
+    input:
+    val(meta)
+
+    output:
+    tuple val(meta), path("*/nucl_gb.accession2taxid"), emit: accession2taxid
+    tuple val(meta), path("*/names.dmp")              , emit: names
+    tuple val(meta), path("*/nodes.dmp")              , emit: nodes
+    tuple val(meta), path("*")                        , emit: downloadtaxonomy_dir
+    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}"
+    """
+    mkdir ${prefix}
+
+    crabs --download-taxonomy \\
+        --output ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}/nucl_gb.accession2taxid
+    touch ${prefix}/names.dmp
+    touch ${prefix}/nodes.dmp
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/crabs/downloadtaxonomy/meta.yml b/modules/nf-core/crabs/downloadtaxonomy/meta.yml
new file mode 100644
index 00000000000..4a4480a2ae0
--- /dev/null
+++ b/modules/nf-core/crabs/downloadtaxonomy/meta.yml
@@ -0,0 +1,69 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "crabs_downloadtaxonomy"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "crabs":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "https://github.com/gjeunen/reference_database_creator"
+      doi: ""
+      licence: ['MIT']
+      identifier: 
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+  
+  ## TODO nf-core: Delete / customise this example input
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+          
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - bam:
+  #Only when we have meta
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+  ## TODO nf-core: Delete / customise this example output
+    - "*.bam":
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+          
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"
diff --git a/modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test b/modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test
new file mode 100644
index 00000000000..4081178463c
--- /dev/null
+++ b/modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process CRABS_DOWNLOADTAXONOMY"
+    script "../main.nf"
+    process "CRABS_DOWNLOADTAXONOMY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "crabs"
+    tag "crabs/downloadtaxonomy"
+
+    test("download") {
+
+        when {
+            params {
+                module_args = "--exclude 'acc2taxid,taxdump'"
+            }
+            process {
+                """
+                input[0] = [ id:'test' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("download - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ id:'test' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test.snap b/modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1edf37d06ec
--- /dev/null
+++ b/modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test.snap
@@ -0,0 +1,137 @@
+{
+    "download": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "accession2taxid": [
+                    
+                ],
+                "names": [
+                    
+                ],
+                "nodes": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-03T13:56:49.20584"
+    },
+    "download - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                        ]
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                ],
+                "accession2taxid": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "downloadtaxonomy_dir": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                        ]
+                    ]
+                ],
+                "names": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "nodes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                ]
+            },
+            {
+                "CRABS_DOWNLOADTAXONOMY": {
+                    "crabs": "v1.0.7"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-03T14:07:27.923472"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/crabs/downloadtaxonomy/tests/nextflow.config b/modules/nf-core/crabs/downloadtaxonomy/tests/nextflow.config
new file mode 100644
index 00000000000..a570ad5f6c8
--- /dev/null
+++ b/modules/nf-core/crabs/downloadtaxonomy/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: 'CRABS_DOWNLOADTAXONOMY' {
+        ext.args = params.module_args
+    }
+
+}
\ No newline at end of file

From 8e1d1126f7dd174cf5d7f1ba82db910a0b969aa6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 14:42:04 +0900
Subject: [PATCH 16/16] remove dbimport from this PR

---
 .../nf-core/crabs/dbimport/environment.yml    |  5 --
 modules/nf-core/crabs/dbimport/main.nf        | 59 -------------
 modules/nf-core/crabs/dbimport/meta.yml       | 52 ------------
 .../nf-core/crabs/dbimport/tests/main.nf.test | 84 -------------------
 .../crabs/dbimport/tests/main.nf.test.snap    | 63 --------------
 .../crabs/dbimport/tests/nextflow.config      |  7 --
 6 files changed, 270 deletions(-)
 delete mode 100644 modules/nf-core/crabs/dbimport/environment.yml
 delete mode 100644 modules/nf-core/crabs/dbimport/main.nf
 delete mode 100644 modules/nf-core/crabs/dbimport/meta.yml
 delete mode 100644 modules/nf-core/crabs/dbimport/tests/main.nf.test
 delete mode 100644 modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/crabs/dbimport/tests/nextflow.config

diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
deleted file mode 100644
index c9761a2d14b..00000000000
--- a/modules/nf-core/crabs/dbimport/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::crabs=1.0.7
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
deleted file mode 100644
index ef00aea503f..00000000000
--- a/modules/nf-core/crabs/dbimport/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-process CRABS_DBIMPORT {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/crabs:1.0.7--pyhdfd78af_0':
-        'biocontainers/crabs:1.0.7--pyhdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(fasta)
-    tuple val(meta2), path(accession2taxid)
-    tuple val(meta3), path(names)
-    tuple val(meta4), path(nodes)
-
-    output:
-    tuple val(meta), path("*.fa"), emit: fasta
-    path "versions.yml"          , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args          = task.ext.args ?: ''
-    def prefix        = task.ext.prefix ?: "${meta.id}"
-    def is_compressed = fasta.name.endsWith(".gz")
-    def fasta_name    = fasta.name.replace(".gz", "")
-    """
-    if [ "${is_compressed}" == "true" ]; then
-        gzip -c -d ${fasta} > ${fasta_name}
-    fi
-
-    crabs --import \\
-        --input ${fasta_name} \\
-        --output ${prefix}.crabsdb.fa \\
-        --acc2tax ${accession2taxid} \\
-        --names ${names} \\
-        --nodes ${nodes} \\
-        $args
-
-    rm ${fasta_name}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.fa
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/crabs/dbimport/meta.yml b/modules/nf-core/crabs/dbimport/meta.yml
deleted file mode 100644
index 0aeffde1558..00000000000
--- a/modules/nf-core/crabs/dbimport/meta.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-name: crabs_dbimport
-description: In-house generated or curated data can be imported into CRABS.
-keywords:
-  - insilico
-  - amplicon
-  - sequencing
-  - inhouse
-tools:
-  - crabs:
-      description: |
-        Crabs (Creating Reference databases for Amplicon-Based Sequencing)
-        is a program to download and curate reference databases
-        for eDNA metabarcoding analyses
-      homepage: https://github.com/gjeunen/reference_database_creator
-      documentation: https://github.com/gjeunen/reference_database_creator?tab=readme-ov-file#running-crabs
-      tool_dev_url: https://github.com/gjeunen/reference_database_creator
-      doi: 10.1111/1755-0998.13741
-      licence: ["MIT License"]
-      identifier: ""
-
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1' ]`
-    - fasta:
-        type: file
-        description: In-house sequencing data
-        pattern: "*.{fa,fasta}"
-output:
-  - fasta:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1' ]`
-      - "*.fa":
-          type: file
-          description: Reverse complemented Sequence
-          pattern: "*.{fa,fasta}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
-authors:
-  - "@famosab"
-  - "@a4000"
-maintainers:
-  - "@famosab"
-  - "@a4000"
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test b/modules/nf-core/crabs/dbimport/tests/main.nf.test
deleted file mode 100644
index b9f50699511..00000000000
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test
+++ /dev/null
@@ -1,84 +0,0 @@
-nextflow_process {
-
-    name "Test Process CRABS_DBIMPORT"
-    script "../main.nf"
-    process "CRABS_DBIMPORT"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "crabs"
-    tag "crabs/dbimport"
-    tag "crabs/downloadtaxonomy"
-
-    setup {
-        run("CRABS_DOWNLOADTAXONOMY") {
-            script "../../downloadtaxonomy/main.nf"
-            process {
-                """
-                input[0] = [ id:'taxonomy' ]
-                """
-            }
-        }
-    }
-
-    test("sarscov2 - fasta") {
-
-        config "./nextflow.config"
-
-        when {
-            params {
-                module_args = "--import-format embl --ranks 'superkingdom;phylum;class;order;family;genus;species' \\"
-            }
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ]
-                input[1] = CRABS_DOWNLOADTAXONOMY.out.accession2taxid
-                input[2] = CRABS_DOWNLOADTAXONOMY.out.names
-                input[3] = CRABS_DOWNLOADTAXONOMY.out.nodes
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - 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)
-                ]
-                input[1] = CRABS_DOWNLOADTAXONOMY.out.accession2taxid
-                input[2] = CRABS_DOWNLOADTAXONOMY.out.names
-                input[3] = CRABS_DOWNLOADTAXONOMY.out.nodes
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
-            )
-        }
-
-    }
-
-}
\ No newline at end of file
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
deleted file mode 100644
index 54f52067cb6..00000000000
--- a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
+++ /dev/null
@@ -1,63 +0,0 @@
-{
-    "sarscov2 - fasta - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,65a68b87678624e13a185da907b3be67"
-                ],
-                "fasta": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,65a68b87678624e13a185da907b3be67"
-                ]
-            },
-            {
-                "CRABS_DBIMPORT": {
-                    "crabs": "v1.0.7"
-                }
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-02-03T13:52:33.256766"
-    },
-    "sarscov2 - fasta": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "fasta": [
-                    
-                ],
-                "versions": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-02-03T14:15:02.785883"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/crabs/dbimport/tests/nextflow.config b/modules/nf-core/crabs/dbimport/tests/nextflow.config
deleted file mode 100644
index 9d003f3db15..00000000000
--- a/modules/nf-core/crabs/dbimport/tests/nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-process {
-
-    withName: CRABS_DBIMPORT {
-        ext.args = params.module_args
-    }
-
-}