From 9f8daa30ac3afa7ef1c1c36c44549860e8369b3f Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 28 Jun 2024 10:57:09 +0200
Subject: [PATCH 01/10] Add the new module nanoq

---
 modules/nf-core/nanoq/environment.yml         |   9 +
 modules/nf-core/nanoq/main.nf                 |  74 +++++
 modules/nf-core/nanoq/meta.yml                |  61 ++++
 modules/nf-core/nanoq/tests/main.nf.test      | 122 +++++++
 modules/nf-core/nanoq/tests/main.nf.test.snap | 307 ++++++++++++++++++
 modules/nf-core/nanoq/tests/tags.yml          |   2 +
 6 files changed, 575 insertions(+)
 create mode 100644 modules/nf-core/nanoq/environment.yml
 create mode 100644 modules/nf-core/nanoq/main.nf
 create mode 100644 modules/nf-core/nanoq/meta.yml
 create mode 100644 modules/nf-core/nanoq/tests/main.nf.test
 create mode 100644 modules/nf-core/nanoq/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/nanoq/tests/tags.yml

diff --git a/modules/nf-core/nanoq/environment.yml b/modules/nf-core/nanoq/environment.yml
new file mode 100644
index 00000000000..41448d5b31d
--- /dev/null
+++ b/modules/nf-core/nanoq/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "nanoq"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::nanoq=0.10.0"
diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
new file mode 100644
index 00000000000..3024e2845fd
--- /dev/null
+++ b/modules/nf-core/nanoq/main.nf
@@ -0,0 +1,74 @@
+process NANOQ {
+
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nanoq:0.10.0--h031d066_2' :
+        'biocontainers/nanoq:0.10.0--h031d066_2'}"
+
+    input:
+    tuple val(meta), path(ontreads)
+    val(output_type) // u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
+
+    output:
+    tuple val(meta), path("*.stats")                                                  , emit: stats
+    tuple val(meta), path("*")                                                        , emit: reads
+    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 seq_type = ontreads.baseName.split("\\.")[1]
+
+    if (output_type == 'u') {
+        output_ext = ""
+    } else if (output_type == 'b') {
+        output_ext = ".bz2"
+    } else if (output_type == 'g') {
+        output_ext = ".gz"
+    } else if (output_type == 'l') {
+        output_ext = ".lzma"
+    }
+
+    """
+    nanoq -i $ontreads \\
+        -r ${prefix}.stats \\
+        -O $output_type \\
+        -o ${prefix}_nanoq.${seq_type}${output_ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanoq: \$(nanoq --version | sed -e 's/nanoq //g')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def seq_type = ontreads.baseName.split("\\.")[1]
+    if (output_type == 'u') {
+        output_ext = ""
+    } else if (output_type == 'b') {
+        output_ext = ".bz2"
+    } else if (output_type == 'g') {
+        output_ext = ".gz"
+    } else if (output_type == 'l') {
+        output_ext = ".lzma"
+    }
+
+    """
+    touch ${prefix}_nanoq.${seq_type}${output_ext}
+    touch ${prefix}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nanoq: \$(nanoq --version | sed -e 's/nanoq //g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml
new file mode 100644
index 00000000000..4910bfd9a0e
--- /dev/null
+++ b/modules/nf-core/nanoq/meta.yml
@@ -0,0 +1,61 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "nanoq"
+description: Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads.
+keywords:
+  - nanoq
+  - Read filters
+  - Read trimming
+  - Read report
+tools:
+  - "nanoq":
+      description: "Ultra-fast quality control and summary reports for nanopore reads"
+      homepage: "https://github.com/esteinig/nanoq"
+      documentation: "https://github.com/esteinig/nanoq"
+      tool_dev_url: "https://github.com/esteinig/nanoq"
+      doi: "10.21105/joss.02991"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - ontreads:
+      type: file
+      description: Compressed or uncompressed nanopore reads in fasta or fastq formats.
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}"
+
+  - output_type:
+      type: string
+      description: "Specifies the output compression type: 'b' for Bzip2, 'g' for gzip, 'l' for Lzma, and 'u' for uncompressed."
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.lzma}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - stats:
+      type: file
+      description: Summary report of reads statistics.
+      pattern: "*.stats"
+
+  - reads:
+      type: file
+      description: Filtered reads.
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.lzma}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@LilyAnderssonLee"
+maintainers:
+  - "@LilyAnderssonLee"
diff --git a/modules/nf-core/nanoq/tests/main.nf.test b/modules/nf-core/nanoq/tests/main.nf.test
new file mode 100644
index 00000000000..9f551cb982f
--- /dev/null
+++ b/modules/nf-core/nanoq/tests/main.nf.test
@@ -0,0 +1,122 @@
+nextflow_process {
+
+    name "Test Process NANOQ"
+    script "../main.nf"
+    process "NANOQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "nanoq"
+
+    test("sarscov2 - nanopore_uncompressed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+
+                input[1] = 'u'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - nanopore_compressed_gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = 'g'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    test("sarscov2 - nanopore_uncompressed_bz2") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = 'b'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    test("sarscov2 - nanopore_uncompressed_lzma") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = 'l'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - nanopore - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    ]
+                    input[1] = 'g'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/nanoq/tests/main.nf.test.snap b/modules/nf-core/nanoq/tests/main.nf.test.snap
new file mode 100644
index 00000000000..6963c22fd2e
--- /dev/null
+++ b/modules/nf-core/nanoq/tests/main.nf.test.snap
@@ -0,0 +1,307 @@
+{
+    "sarscov2 - nanopore_compressed_gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-06-28T10:54:00.467634"
+    },
+    "sarscov2 - nanopore_uncompressed_bz2": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-06-28T10:54:04.660873"
+    },
+    "sarscov2 - nanopore - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "/Users/lili.li.2/modules/.nf-test/tests/9d4f60427672ca3da40466350f6c67ae/work/08/8e3658c9a4909104a7edb60966757c/test_nanoq.fastq.gz",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "/Users/lili.li.2/modules/.nf-test/tests/9d4f60427672ca3da40466350f6c67ae/work/08/8e3658c9a4909104a7edb60966757c/test_nanoq.fastq.gz",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-06-28T10:55:28.522754"
+    },
+    "sarscov2 - nanopore_uncompressed_lzma": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-06-28T10:54:08.886135"
+    },
+    "sarscov2 - nanopore_uncompressed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
+                            "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76",
+                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                        ]
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-06-28T10:53:56.126459"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/nanoq/tests/tags.yml b/modules/nf-core/nanoq/tests/tags.yml
new file mode 100644
index 00000000000..37457df1765
--- /dev/null
+++ b/modules/nf-core/nanoq/tests/tags.yml
@@ -0,0 +1,2 @@
+nanoq:
+  - "modules/nf-core/nanoq/**"

From e3f932a6d1563421db82ba4dd380167762c78e69 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 28 Jun 2024 12:55:15 +0200
Subject: [PATCH 02/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 3024e2845fd..67eb742016f 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -4,7 +4,6 @@ process NANOQ {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/nanoq:0.10.0--h031d066_2' :
         'biocontainers/nanoq:0.10.0--h031d066_2'}"

From a26f675236e2bad2c82f5f0c9b7822ee22abe1a3 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 28 Jun 2024 12:55:20 +0200
Subject: [PATCH 03/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 67eb742016f..479791607fb 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -1,5 +1,4 @@
 process NANOQ {
-
     tag "$meta.id"
     label 'process_low'
 

From b06b9a46517c17767a21ffd853b153a092461027 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 28 Jun 2024 15:03:03 +0200
Subject: [PATCH 04/10] define the output_format

---
 modules/nf-core/nanoq/main.nf                 | 30 +------
 modules/nf-core/nanoq/meta.yml                |  7 +-
 modules/nf-core/nanoq/tests/main.nf.test      | 16 ++--
 modules/nf-core/nanoq/tests/main.nf.test.snap | 84 +++++--------------
 4 files changed, 37 insertions(+), 100 deletions(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 479791607fb..a2bfeec5c1d 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -9,11 +9,11 @@ process NANOQ {
 
     input:
     tuple val(meta), path(ontreads)
-    val(output_type) // u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
+    val(output_format) //One of the following: fastq, fastq.gz, fastq.bz2, fastq.lzma, fasta, fasta.gz, fasta.bz2, fasta.lzma.
 
     output:
     tuple val(meta), path("*.stats")                                                  , emit: stats
-    tuple val(meta), path("*")                                                        , emit: reads
+    tuple val(meta), path("*_nanoq.${output_format}")                                                 , emit: reads
     path "versions.yml"                                                               , emit: versions
 
     when:
@@ -22,23 +22,11 @@ process NANOQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_type = ontreads.baseName.split("\\.")[1]
-
-    if (output_type == 'u') {
-        output_ext = ""
-    } else if (output_type == 'b') {
-        output_ext = ".bz2"
-    } else if (output_type == 'g') {
-        output_ext = ".gz"
-    } else if (output_type == 'l') {
-        output_ext = ".lzma"
-    }
 
     """
     nanoq -i $ontreads \\
         -r ${prefix}.stats \\
-        -O $output_type \\
-        -o ${prefix}_nanoq.${seq_type}${output_ext}
+        -o ${prefix}_nanoq.$output_format
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -49,19 +37,9 @@ process NANOQ {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_type = ontreads.baseName.split("\\.")[1]
-    if (output_type == 'u') {
-        output_ext = ""
-    } else if (output_type == 'b') {
-        output_ext = ".bz2"
-    } else if (output_type == 'g') {
-        output_ext = ".gz"
-    } else if (output_type == 'l') {
-        output_ext = ".lzma"
-    }
 
     """
-    touch ${prefix}_nanoq.${seq_type}${output_ext}
+    touch ${prefix}_nanoq.$output_format
     touch ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml
index 4910bfd9a0e..87fd2f41d9e 100644
--- a/modules/nf-core/nanoq/meta.yml
+++ b/modules/nf-core/nanoq/meta.yml
@@ -28,10 +28,9 @@ input:
       description: Compressed or uncompressed nanopore reads in fasta or fastq formats.
       pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}"
 
-  - output_type:
+  - output_format:
       type: string
-      description: "Specifies the output compression type: 'b' for Bzip2, 'g' for gzip, 'l' for Lzma, and 'u' for uncompressed."
-      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.lzma}"
+      description: "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma."
 
 output:
   - meta:
@@ -48,7 +47,7 @@ output:
   - reads:
       type: file
       description: Filtered reads.
-      pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.lzma}"
+      pattern: "*.{fasta,fastq}{,.gz,.bz2,.lzma}"
 
   - versions:
       type: file
diff --git a/modules/nf-core/nanoq/tests/main.nf.test b/modules/nf-core/nanoq/tests/main.nf.test
index 9f551cb982f..1dfbae33740 100644
--- a/modules/nf-core/nanoq/tests/main.nf.test
+++ b/modules/nf-core/nanoq/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                     file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
                 ]
 
-                input[1] = 'u'
+                input[1] = 'fastq'
                 """
             }
         }
@@ -40,7 +40,7 @@ nextflow_process {
                     [ id:'test', single_end:true ], // meta map
                     file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
                 ]
-                input[1] = 'g'
+                input[1] = 'fastq.gz'
                 """
             }
         }
@@ -52,7 +52,7 @@ nextflow_process {
             )
         }
     }
-    test("sarscov2 - nanopore_uncompressed_bz2") {
+    test("sarscov2 - nanopore_compressed_bz2") {
 
         when {
             process {
@@ -61,7 +61,7 @@ nextflow_process {
                     [ id:'test', single_end:true ], // meta map
                     file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
                 ]
-                input[1] = 'b'
+                input[1] = 'fastq.bz2'
                 """
             }
         }
@@ -73,7 +73,7 @@ nextflow_process {
             )
         }
     }
-    test("sarscov2 - nanopore_uncompressed_lzma") {
+    test("sarscov2 - nanopore_compressed_lzma") {
 
         when {
             process {
@@ -82,7 +82,7 @@ nextflow_process {
                     [ id:'test', single_end:true ], // meta map
                     file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
                 ]
-                input[1] = 'l'
+                input[1] = 'fastq.lzma'
                 """
             }
         }
@@ -95,7 +95,7 @@ nextflow_process {
         }
     }
 
-    test("sarscov2 - nanopore - stub") {
+    test("sarscov2 - nanopore_compressed_gz - stub") {
 
         options "-stub"
 
@@ -106,7 +106,7 @@ nextflow_process {
                     [ id:'test', single_end:true ], // meta map
                     file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
                     ]
-                    input[1] = 'g'
+                    input[1] = 'fastq.gz'
                 """
             }
         }
diff --git a/modules/nf-core/nanoq/tests/main.nf.test.snap b/modules/nf-core/nanoq/tests/main.nf.test.snap
index 6963c22fd2e..7c1c4b8e17e 100644
--- a/modules/nf-core/nanoq/tests/main.nf.test.snap
+++ b/modules/nf-core/nanoq/tests/main.nf.test.snap
@@ -17,11 +17,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "2": [
@@ -33,11 +29,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "stats": [
@@ -58,9 +50,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T10:54:00.467634"
+        "timestamp": "2024-06-28T15:00:12.054286"
     },
-    "sarscov2 - nanopore_uncompressed_bz2": {
+    "sarscov2 - nanopore_compressed_gz - stub": {
         "content": [
             {
                 "0": [
@@ -69,7 +61,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -78,11 +70,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "/Users/lili.li.2/modules/.nf-test/tests/e49c0ef96ddc521ecea9b6c6c7044d8f/work/2f/376d5b8d15822f792cec16483ce364/test_nanoq.fastq.gz"
                     ]
                 ],
                 "2": [
@@ -94,11 +82,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "/Users/lili.li.2/modules/.nf-test/tests/e49c0ef96ddc521ecea9b6c6c7044d8f/work/2f/376d5b8d15822f792cec16483ce364/test_nanoq.fastq.gz"
                     ]
                 ],
                 "stats": [
@@ -107,7 +91,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -119,9 +103,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T10:54:04.660873"
+        "timestamp": "2024-06-28T15:01:40.834668"
     },
-    "sarscov2 - nanopore - stub": {
+    "sarscov2 - nanopore_compressed_bz2": {
         "content": [
             {
                 "0": [
@@ -130,7 +114,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -139,11 +123,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "/Users/lili.li.2/modules/.nf-test/tests/9d4f60427672ca3da40466350f6c67ae/work/08/8e3658c9a4909104a7edb60966757c/test_nanoq.fastq.gz",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
                     ]
                 ],
                 "2": [
@@ -155,11 +135,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "/Users/lili.li.2/modules/.nf-test/tests/9d4f60427672ca3da40466350f6c67ae/work/08/8e3658c9a4909104a7edb60966757c/test_nanoq.fastq.gz",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
                     ]
                 ],
                 "stats": [
@@ -168,7 +144,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -180,9 +156,9 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T10:55:28.522754"
+        "timestamp": "2024-06-28T15:00:16.575041"
     },
-    "sarscov2 - nanopore_uncompressed_lzma": {
+    "sarscov2 - nanopore_compressed_lzma": {
         "content": [
             {
                 "0": [
@@ -200,11 +176,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
                     ]
                 ],
                 "2": [
@@ -216,11 +188,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
                     ]
                 ],
                 "stats": [
@@ -241,7 +209,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T10:54:08.886135"
+        "timestamp": "2024-06-28T15:00:20.907827"
     },
     "sarscov2 - nanopore_uncompressed": {
         "content": [
@@ -261,11 +229,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "2": [
@@ -277,11 +241,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe",
-                            "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76",
-                            "versions.yml:md5,7a40efe417ff7dbb9e91e9c1629a04e6"
-                        ]
+                        "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "stats": [
@@ -302,6 +262,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T10:53:56.126459"
+        "timestamp": "2024-06-28T15:00:07.933329"
     }
 }
\ No newline at end of file

From 4ea90b5de2d8ec4d7ea4fe8db8614b6d080468bb Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Tue, 2 Jul 2024 09:47:46 +0200
Subject: [PATCH 05/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index a2bfeec5c1d..248b0dd18b4 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -26,7 +26,7 @@ process NANOQ {
     """
     nanoq -i $ontreads \\
         -r ${prefix}.stats \\
-        -o ${prefix}_nanoq.$output_format
+        -o ${prefix}.$output_format
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 4f184dccac57dce02e155c8380d9e6a04e31cc4b Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Tue, 2 Jul 2024 09:47:51 +0200
Subject: [PATCH 06/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 248b0dd18b4..e5d0261063f 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -21,7 +21,7 @@ process NANOQ {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
 
     """
     nanoq -i $ontreads \\

From 0b35d7eaecb53ba70e42864a8e006ec720ff881d Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Tue, 2 Jul 2024 09:48:07 +0200
Subject: [PATCH 07/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index e5d0261063f..3fbb1963624 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -39,7 +39,7 @@ process NANOQ {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    touch ${prefix}_nanoq.$output_format
+    echo "" | gzip > ${prefix}_nanoq.$output_format
     touch ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml

From d1b11c99c08335691b8a7bbdccb3bdeb26a10434 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Tue, 2 Jul 2024 10:02:55 +0200
Subject: [PATCH 08/10] update the stub run with gzip

---
 modules/nf-core/nanoq/main.nf                 |  6 ++--
 modules/nf-core/nanoq/tests/main.nf.test.snap | 34 +++++++++----------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 3fbb1963624..3b6d719ab6a 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -13,7 +13,7 @@ process NANOQ {
 
     output:
     tuple val(meta), path("*.stats")                                                  , emit: stats
-    tuple val(meta), path("*_nanoq.${output_format}")                                                 , emit: reads
+    tuple val(meta), path("*_nanoq.${output_format}")                                 , emit: reads
     path "versions.yml"                                                               , emit: versions
 
     when:
@@ -36,10 +36,10 @@ process NANOQ {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
 
     """
-    echo "" | gzip > ${prefix}_nanoq.$output_format
+    echo "" | gzip > ${prefix}.$output_format
     touch ${prefix}.stats
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/nanoq/tests/main.nf.test.snap b/modules/nf-core/nanoq/tests/main.nf.test.snap
index 7c1c4b8e17e..e9f6b8b5453 100644
--- a/modules/nf-core/nanoq/tests/main.nf.test.snap
+++ b/modules/nf-core/nanoq/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -38,7 +38,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -50,7 +50,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T15:00:12.054286"
+        "timestamp": "2024-07-02T10:00:12.328317"
     },
     "sarscov2 - nanopore_compressed_gz - stub": {
         "content": [
@@ -61,7 +61,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_nanoq.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -70,7 +70,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "/Users/lili.li.2/modules/.nf-test/tests/e49c0ef96ddc521ecea9b6c6c7044d8f/work/2f/376d5b8d15822f792cec16483ce364/test_nanoq.fastq.gz"
+                        "test_nanoq.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "2": [
@@ -82,7 +82,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "/Users/lili.li.2/modules/.nf-test/tests/e49c0ef96ddc521ecea9b6c6c7044d8f/work/2f/376d5b8d15822f792cec16483ce364/test_nanoq.fastq.gz"
+                        "test_nanoq.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "stats": [
@@ -91,7 +91,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_nanoq.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -103,7 +103,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T15:01:40.834668"
+        "timestamp": "2024-07-02T10:00:24.873908"
     },
     "sarscov2 - nanopore_compressed_bz2": {
         "content": [
@@ -114,7 +114,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -144,7 +144,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -156,7 +156,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T15:00:16.575041"
+        "timestamp": "2024-07-02T10:00:16.460467"
     },
     "sarscov2 - nanopore_compressed_lzma": {
         "content": [
@@ -167,7 +167,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -197,7 +197,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -209,7 +209,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T15:00:20.907827"
+        "timestamp": "2024-07-02T10:00:20.825269"
     },
     "sarscov2 - nanopore_uncompressed": {
         "content": [
@@ -220,7 +220,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -250,7 +250,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -262,6 +262,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-06-28T15:00:07.933329"
+        "timestamp": "2024-07-02T10:00:07.8772"
     }
 }
\ No newline at end of file

From df9cfc4a7a837acb055582782debdf18f05fc275 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Tue, 2 Jul 2024 13:41:28 +0200
Subject: [PATCH 09/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 3b6d719ab6a..f0fff961f63 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -37,7 +37,6 @@ process NANOQ {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
-
     """
     echo "" | gzip > ${prefix}.$output_format
     touch ${prefix}.stats

From a74803dfea652f2d3b0081a13d466cc0806213c1 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Tue, 2 Jul 2024 13:41:35 +0200
Subject: [PATCH 10/10] Update modules/nf-core/nanoq/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/nanoq/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index f0fff961f63..298ede2b7bc 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -22,7 +22,6 @@ process NANOQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
-
     """
     nanoq -i $ontreads \\
         -r ${prefix}.stats \\