From 20093da6d6b79857e66276e04329ec123f34a73e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 12:32:49 +0200
Subject: [PATCH 01/17] add crabs module

---
 .../nf-core/crabs/insilicopcr/environment.yml |  7 ++
 modules/nf-core/crabs/insilicopcr/main.nf     | 48 +++++++++++++
 modules/nf-core/crabs/insilicopcr/meta.yml    | 49 +++++++++++++
 .../crabs/insilicopcr/tests/main.nf.test      | 59 ++++++++++++++++
 .../crabs/insilicopcr/tests/main.nf.test.snap | 68 +++++++++++++++++++
 .../crabs/insilicopcr/tests/nextflow.config   |  7 ++
 .../nf-core/crabs/insilicopcr/tests/tags.yml  |  2 +
 7 files changed, 240 insertions(+)
 create mode 100644 modules/nf-core/crabs/insilicopcr/environment.yml
 create mode 100644 modules/nf-core/crabs/insilicopcr/main.nf
 create mode 100644 modules/nf-core/crabs/insilicopcr/meta.yml
 create mode 100644 modules/nf-core/crabs/insilicopcr/tests/main.nf.test
 create mode 100644 modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/crabs/insilicopcr/tests/nextflow.config
 create mode 100644 modules/nf-core/crabs/insilicopcr/tests/tags.yml

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
new file mode 100644
index 00000000000..7e3f76355b9
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/environment.yml
@@ -0,0 +1,7 @@
+name: crabs_insilicopcr
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::crabs=0.1.1"
diff --git a/modules/nf-core/crabs/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
new file mode 100644
index 00000000000..58e9115c2bd
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -0,0 +1,48 @@
+process CRABS_INSILICOPCR {
+    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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
+        'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.{fa,fasta}"), emit: fasta
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args    = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    crabs insilico_pcr \\
+        --input $fasta \\
+        --output ${prefix}.crabs.fa \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${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/insilicopcr/meta.yml b/modules/nf-core/crabs/insilicopcr/meta.yml
new file mode 100644
index 00000000000..2bc55970f7f
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/meta.yml
@@ -0,0 +1,49 @@
+name: crabs_insilicopcr
+description: CRABS extracts the amplicon region of the primer set by conducting an in silico PCR.
+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: Sequence to conduct in silico PCR on
+      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 amplified Sequence
+      pattern: "*.{fa,fasta}"
+
+authors:
+  - "@famosab"
+  - "@a4000"
+maintainers:
+  - "@famosab"
+  - "@a4000"
diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
new file mode 100644
index 00000000000..a5dbbea5d91
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process CRABS_INSILICOPCR"
+    script "../main.nf"
+    process "CRABS_INSILICOPCR"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "crabs"
+    tag "crabs/insilicopcr"
+
+    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() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
new file mode 100644
index 00000000000..4882f9d8d00
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T12:28:13.221768"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.crabs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.crabs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T12:28:03.538411"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/crabs/insilicopcr/tests/nextflow.config b/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
new file mode 100644
index 00000000000..2c4957ee8bc
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: CRABS_INSILICOPCR {
+        ext.args = '--fwd "GTCGGTAAAACTCGTGCCAGC" --rev "CATAGTGGGGTATCTAATCCCAGTTTG" --error 4.5'
+    }
+
+}
diff --git a/modules/nf-core/crabs/insilicopcr/tests/tags.yml b/modules/nf-core/crabs/insilicopcr/tests/tags.yml
new file mode 100644
index 00000000000..6681558e3c9
--- /dev/null
+++ b/modules/nf-core/crabs/insilicopcr/tests/tags.yml
@@ -0,0 +1,2 @@
+crabs/insilicopcr:
+  - "modules/nf-core/crabs/insilicopcr/**"

From 058cd2a3695ac07d5a23b003200c595fcb1bde2b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 12:47:06 +0200
Subject: [PATCH 02/17] threads prettier

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

diff --git a/modules/nf-core/crabs/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
index 58e9115c2bd..f2b6c79fc29 100644
--- a/modules/nf-core/crabs/insilicopcr/main.nf
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -26,6 +26,7 @@ process CRABS_INSILICOPCR {
     crabs insilico_pcr \\
         --input $fasta \\
         --output ${prefix}.crabs.fa \\
+        -t ${task.cpus} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/crabs/insilicopcr/meta.yml b/modules/nf-core/crabs/insilicopcr/meta.yml
index 2bc55970f7f..3fb6734472c 100644
--- a/modules/nf-core/crabs/insilicopcr/meta.yml
+++ b/modules/nf-core/crabs/insilicopcr/meta.yml
@@ -13,7 +13,7 @@ tools:
       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']
+      licence: ["MIT License"]
 
 input:
   - meta:

From d40695a2a2bc8a0d32fa8b27b6d204d479361560 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 14:48:03 +0200
Subject: [PATCH 03/17] fix test and linting

---
 modules/nf-core/crabs/insilicopcr/main.nf     |  2 +-
 modules/nf-core/crabs/insilicopcr/meta.yml    |  2 ++
 .../crabs/insilicopcr/tests/main.nf.test      |  6 +++-
 .../crabs/insilicopcr/tests/main.nf.test.snap | 30 ++++---------------
 4 files changed, 13 insertions(+), 27 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
index f2b6c79fc29..f4edad275e6 100644
--- a/modules/nf-core/crabs/insilicopcr/main.nf
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -26,7 +26,7 @@ process CRABS_INSILICOPCR {
     crabs insilico_pcr \\
         --input $fasta \\
         --output ${prefix}.crabs.fa \\
-        -t ${task.cpus} \\
+        --threads ${task.cpus} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/crabs/insilicopcr/meta.yml b/modules/nf-core/crabs/insilicopcr/meta.yml
index 3fb6734472c..ce362940d3a 100644
--- a/modules/nf-core/crabs/insilicopcr/meta.yml
+++ b/modules/nf-core/crabs/insilicopcr/meta.yml
@@ -3,6 +3,8 @@ description: CRABS extracts the amplicon region of the primer set by conducting
 keywords:
   - insilico
   - PCR
+  - amplicon
+  - sequencing
 tools:
   - crabs:
       description: |
diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
index a5dbbea5d91..5296b0e7aba 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
@@ -26,7 +26,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.fasta[0][1]).name,
+                    ).match()
+                    }
             )
         }
 
diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
index 4882f9d8d00..a7a3ff6a32d 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
@@ -34,35 +34,15 @@
     },
     "sarscov2 - fasta": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.crabs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
-                ],
-                "fasta": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.crabs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
-                ]
-            }
+            [
+                "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+            ],
+            "test.crabs.fa"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T12:28:03.538411"
+        "timestamp": "2024-09-05T14:46:51.816788"
     }
 }
\ No newline at end of file

From 5b9e4d5530560809fc5e8ec7176ad6bc011e470d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 14:57:40 +0200
Subject: [PATCH 04/17] remove defaults

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

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 7e3f76355b9..1533ca9a8b7 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/environment.yml
@@ -2,6 +2,5 @@ name: crabs_insilicopcr
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::crabs=0.1.1"

From f53f85a89d80d48ce8345d0596061bba94549f46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 15:23:29 +0200
Subject: [PATCH 05/17] update crabs with wave containers

---
 modules/nf-core/crabs/insilicopcr/environment.yml     |  7 ++++++-
 modules/nf-core/crabs/insilicopcr/main.nf             | 11 ++++-------
 .../nf-core/crabs/insilicopcr/tests/main.nf.test.snap | 10 +++++-----
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 1533ca9a8b7..62dbe07d2bc 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/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/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
index f4edad275e6..cec42e1e9b4 100644
--- a/modules/nf-core/crabs/insilicopcr/main.nf
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -2,11 +2,10 @@ process CRABS_INSILICOPCR {
     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_INSILICOPCR {
     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.
     """
     crabs insilico_pcr \\
         --input $fasta \\
@@ -31,19 +29,18 @@ process CRABS_INSILICOPCR {
 
     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/insilicopcr/tests/main.nf.test.snap b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
index a7a3ff6a32d..45137914014 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                    "versions.yml:md5,688cca24ee493f8c07e5e069e20fea10"
                 ],
                 "fasta": [
                     [
@@ -22,7 +22,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                    "versions.yml:md5,688cca24ee493f8c07e5e069e20fea10"
                 ]
             }
         ],
@@ -30,12 +30,12 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T12:28:13.221768"
+        "timestamp": "2024-09-05T15:22:18.567813"
     },
     "sarscov2 - fasta": {
         "content": [
             [
-                "versions.yml:md5,d334dbe811797a5944b67d096b125b7c"
+                "versions.yml:md5,688cca24ee493f8c07e5e069e20fea10"
             ],
             "test.crabs.fa"
         ],
@@ -43,6 +43,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T14:46:51.816788"
+        "timestamp": "2024-09-05T15:22:12.207826"
     }
 }
\ No newline at end of file

From dacd9a28056ba2e41b55680c250d13ff5e08f552 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Thu, 5 Sep 2024 15:41:25 +0200
Subject: [PATCH 06/17] update meta

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

diff --git a/modules/nf-core/crabs/insilicopcr/meta.yml b/modules/nf-core/crabs/insilicopcr/meta.yml
index ce362940d3a..f7d0d8121a2 100644
--- a/modules/nf-core/crabs/insilicopcr/meta.yml
+++ b/modules/nf-core/crabs/insilicopcr/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 7262a0e3abf970b84adaef0c6bd0aaf9d362fad7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:06:53 +0200
Subject: [PATCH 07/17] remove name

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

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 62dbe07d2bc..78a9b98db33 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/environment.yml
@@ -1,4 +1,3 @@
-name: crabs_insilicopcr
 channels:
   - conda-forge
   - bioconda

From e2d3075db4568cfe18618c5795e051a6e2f38e7f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:33:50 +0200
Subject: [PATCH 08/17] update env

---
 modules/nf-core/crabs/insilicopcr/environment.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 78a9b98db33..489866b9e39 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/environment.yml
@@ -2,9 +2,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - wget=1.21.3
-  - muscle=3.8.31
-  - cutadapt>=4.0
-  - vsearch>=2.13.3
+  - 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 edfdf925de61f3a2dd7dac9416b559c3f571d8d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:36:49 +0200
Subject: [PATCH 09/17] prettier

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

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

From c43e41f9ad143af708b4944f2ea22809e38e415d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 9 Sep 2024 09:45:14 +0200
Subject: [PATCH 10/17] fix pip version

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

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 5bbf98b7f43..ceed5f98e28 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/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 0d8c243f44be17b95bffda5b162200a959307edf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 25 Oct 2024 13:00:15 +0200
Subject: [PATCH 11/17] update to 1.0.4 errors in test still exist

---
 modules/nf-core/crabs/insilicopcr/environment.yml         | 8 +-------
 modules/nf-core/crabs/insilicopcr/main.nf                 | 6 +++---
 modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap | 6 +++---
 modules/nf-core/crabs/insilicopcr/tests/nextflow.config   | 2 +-
 4 files changed, 8 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index ceed5f98e28..20be3a698d8 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/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/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
index cec42e1e9b4..cfa1193bc2b 100644
--- a/modules/nf-core/crabs/insilicopcr/main.nf
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -4,8 +4,8 @@ process CRABS_INSILICOPCR {
 
     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)
@@ -21,7 +21,7 @@ process CRABS_INSILICOPCR {
     def args    = task.ext.args ?: ''
     def prefix  = task.ext.prefix ?: "${meta.id}"
     """
-    crabs insilico_pcr \\
+    crabs --in-silico-pcr \\
         --input $fasta \\
         --output ${prefix}.crabs.fa \\
         --threads ${task.cpus} \\
diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
index 45137914014..ef1ed557a36 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,688cca24ee493f8c07e5e069e20fea10"
+                    "versions.yml:md5,7698551e7ac06a8f18b3ca861d0ec81d"
                 ],
                 "fasta": [
                     [
@@ -22,7 +22,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,688cca24ee493f8c07e5e069e20fea10"
+                    "versions.yml:md5,7698551e7ac06a8f18b3ca861d0ec81d"
                 ]
             }
         ],
@@ -30,7 +30,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T15:22:18.567813"
+        "timestamp": "2024-10-25T12:47:20.344112"
     },
     "sarscov2 - fasta": {
         "content": [
diff --git a/modules/nf-core/crabs/insilicopcr/tests/nextflow.config b/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
index 2c4957ee8bc..8a5ea2077c3 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
+++ b/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
@@ -1,7 +1,7 @@
 process {
 
     withName: CRABS_INSILICOPCR {
-        ext.args = '--fwd "GTCGGTAAAACTCGTGCCAGC" --rev "CATAGTGGGGTATCTAATCCCAGTTTG" --error 4.5'
+        ext.args = '--forward "GTCGGTAAAACTCGTGCCAGC" --reverse "CATAGTGGGGTATCTAATCCCAGTTTG"'
     }
 
 }

From 3537da55bc2584c02ca02b85d0f7b3ce27560321 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 18 Nov 2024 14:27:49 +0100
Subject: [PATCH 12/17] update and fix linting

---
 .../nf-core/crabs/insilicopcr/environment.yml |  2 +-
 modules/nf-core/crabs/insilicopcr/main.nf     |  4 +-
 modules/nf-core/crabs/insilicopcr/meta.yml    | 50 ++++++++++---------
 3 files changed, 29 insertions(+), 27 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 20be3a698d8..74ca9a2d9b3 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/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/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
index cfa1193bc2b..d7f55d41fbd 100644
--- a/modules/nf-core/crabs/insilicopcr/main.nf
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -4,8 +4,8 @@ process CRABS_INSILICOPCR {
 
     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/insilicopcr/meta.yml b/modules/nf-core/crabs/insilicopcr/meta.yml
index f7d0d8121a2..12571e0b5db 100644
--- a/modules/nf-core/crabs/insilicopcr/meta.yml
+++ b/modules/nf-core/crabs/insilicopcr/meta.yml
@@ -1,5 +1,6 @@
 name: crabs_insilicopcr
-description: CRABS extracts the amplicon region of the primer set by conducting an in silico PCR.
+description: CRABS extracts the amplicon region of the primer set by conducting an
+  in silico PCR.
 keywords:
   - insilico
   - PCR
@@ -16,33 +17,34 @@ 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: Sequence to conduct in silico PCR on
-      pattern: "*.{fa,fasta}"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: Sequence to conduct in silico PCR on
+        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 amplified Sequence
-      pattern: "*.{fa,fasta}"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.{fa,fasta}":
+          type: file
+          description: Reverse complemented amplified Sequence
+          pattern: "*.{fa,fasta}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@famosab"
   - "@a4000"

From f830e69aca6ec6f6950979d15c62f809897aa96d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Wed, 20 Nov 2024 12:39:18 +0100
Subject: [PATCH 13/17] change ext args to new convention

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

diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
index 5296b0e7aba..53ab21b0f27 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
@@ -13,6 +13,9 @@ nextflow_process {
     test("sarscov2 - fasta") {
 
         when {
+            params {
+                module_args = '--forward "GTCGGTAAAACTCGTGCCAGC" --reverse "CATAGTGGGGTATCTAATCCCAGTTTG"'
+            }
             process {
                 """
                 input[0] = [
diff --git a/modules/nf-core/crabs/insilicopcr/tests/nextflow.config b/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
index 8a5ea2077c3..9fdb9ed9351 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
+++ b/modules/nf-core/crabs/insilicopcr/tests/nextflow.config
@@ -1,7 +1,7 @@
 process {
 
     withName: CRABS_INSILICOPCR {
-        ext.args = '--forward "GTCGGTAAAACTCGTGCCAGC" --reverse "CATAGTGGGGTATCTAATCCCAGTTTG"'
+        ext.args = params.module_args
     }
 
 }

From d05c9ff2d961b05c68cafb5cc27116364e82e115 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 12:53:07 +0900
Subject: [PATCH 14/17] remove tags yml

---
 modules/nf-core/crabs/insilicopcr/tests/tags.yml | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 modules/nf-core/crabs/insilicopcr/tests/tags.yml

diff --git a/modules/nf-core/crabs/insilicopcr/tests/tags.yml b/modules/nf-core/crabs/insilicopcr/tests/tags.yml
deleted file mode 100644
index 6681558e3c9..00000000000
--- a/modules/nf-core/crabs/insilicopcr/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-crabs/insilicopcr:
-  - "modules/nf-core/crabs/insilicopcr/**"

From 7dddaec008c728f8f1e0177edf527817a4fffe88 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 12:56:03 +0900
Subject: [PATCH 15/17] only use config in real test

---
 modules/nf-core/crabs/insilicopcr/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
index 53ab21b0f27..97fd5662637 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process CRABS_INSILICOPCR"
     script "../main.nf"
     process "CRABS_INSILICOPCR"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -12,6 +11,8 @@ nextflow_process {
 
     test("sarscov2 - fasta") {
 
+        config "./nextflow.config"
+
         when {
             params {
                 module_args = '--forward "GTCGGTAAAACTCGTGCCAGC" --reverse "CATAGTGGGGTATCTAATCCCAGTTTG"'

From 7ffb56c9aef468c7f76e0b0f49f71e2b9bc5fe82 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 3 Feb 2025 14:38:30 +0900
Subject: [PATCH 16/17] update to 1.0.7

---
 modules/nf-core/crabs/insilicopcr/environment.yml |  2 +-
 modules/nf-core/crabs/insilicopcr/main.nf         |  8 ++++----
 .../nf-core/crabs/insilicopcr/tests/main.nf.test  |  5 ++++-
 .../crabs/insilicopcr/tests/main.nf.test.snap     | 15 ++++++++++-----
 4 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/environment.yml b/modules/nf-core/crabs/insilicopcr/environment.yml
index 74ca9a2d9b3..c9761a2d14b 100644
--- a/modules/nf-core/crabs/insilicopcr/environment.yml
+++ b/modules/nf-core/crabs/insilicopcr/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/insilicopcr/main.nf b/modules/nf-core/crabs/insilicopcr/main.nf
index d7f55d41fbd..ef1e9ffa20f 100644
--- a/modules/nf-core/crabs/insilicopcr/main.nf
+++ b/modules/nf-core/crabs/insilicopcr/main.nf
@@ -4,8 +4,8 @@ process CRABS_INSILICOPCR {
 
     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)
@@ -29,7 +29,7 @@ process CRABS_INSILICOPCR {
 
     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
     """
 
@@ -40,7 +40,7 @@ process CRABS_INSILICOPCR {
 
     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/insilicopcr/tests/main.nf.test b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
index 97fd5662637..495ad09ba47 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
@@ -58,7 +58,10 @@ 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/insilicopcr/tests/main.nf.test.snap b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
index ef1ed557a36..8e7460f1058 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7698551e7ac06a8f18b3ca861d0ec81d"
+                    "versions.yml:md5,adee442c0437fa5a481ff3e3b9760a44"
                 ],
                 "fasta": [
                     [
@@ -22,15 +22,20 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7698551e7ac06a8f18b3ca861d0ec81d"
+                    "versions.yml:md5,adee442c0437fa5a481ff3e3b9760a44"
                 ]
+            },
+            {
+                "CRABS_INSILICOPCR": {
+                    "crabs": "v1.0.7"
+                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-25T12:47:20.344112"
+        "timestamp": "2025-02-03T14:34:58.943001"
     },
     "sarscov2 - fasta": {
         "content": [

From b45797cdc75dbdb0317f5faaf9af03fb8fda7c95 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Tue, 18 Feb 2025 13:37:25 +0100
Subject: [PATCH 17/17] update snap

---
 modules/nf-core/crabs/insilicopcr/meta.yml           | 1 -
 modules/nf-core/crabs/insilicopcr/tests/main.nf.test | 9 +++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/crabs/insilicopcr/meta.yml b/modules/nf-core/crabs/insilicopcr/meta.yml
index 12571e0b5db..3510f2f7b87 100644
--- a/modules/nf-core/crabs/insilicopcr/meta.yml
+++ b/modules/nf-core/crabs/insilicopcr/meta.yml
@@ -18,7 +18,6 @@ tools:
       doi: 10.1111/1755-0998.13741
       licence: ["MIT License"]
       identifier: ""
-
 input:
   - - meta:
         type: map
diff --git a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
index 495ad09ba47..26b5b0ba93c 100644
--- a/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
+++ b/modules/nf-core/crabs/insilicopcr/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome-ena.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -34,7 +34,7 @@ nextflow_process {
                     process.out.versions,
                     file(process.out.fasta[0][1]).name,
                     ).match()
-                    }
+                }
             )
         }
 
@@ -49,7 +49,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome-ena.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -61,7 +61,8 @@ nextflow_process {
                 { assert snapshot(
                     process.out,
                     path(process.out.versions[0]).yaml
-                    ).match() }
+                    ).match() 
+                }
             )
         }