From 00e68a26d36a78f908a5d1c084773a55950e9b4e Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Thu, 5 Sep 2024 15:55:58 +0200
Subject: [PATCH 01/22] Add motus prep_long

---
 .../nf-core/motus/preplong/environment.yml    |  7 ++
 modules/nf-core/motus/preplong/main.nf        | 54 +++++++++++++
 modules/nf-core/motus/preplong/meta.yml       | 46 +++++++++++
 .../nf-core/motus/preplong/tests/main.nf.test | 76 +++++++++++++++++++
 .../motus/preplong/tests/main.nf.test.snap    | 72 ++++++++++++++++++
 modules/nf-core/motus/preplong/tests/tags.yml |  2 +
 6 files changed, 257 insertions(+)
 create mode 100644 modules/nf-core/motus/preplong/environment.yml
 create mode 100644 modules/nf-core/motus/preplong/main.nf
 create mode 100644 modules/nf-core/motus/preplong/meta.yml
 create mode 100644 modules/nf-core/motus/preplong/tests/main.nf.test
 create mode 100644 modules/nf-core/motus/preplong/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/motus/preplong/tests/tags.yml

diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml
new file mode 100644
index 00000000000..fa79445404f
--- /dev/null
+++ b/modules/nf-core/motus/preplong/environment.yml
@@ -0,0 +1,7 @@
+name: "motus_preplong"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::motus=3.1.0"
diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
new file mode 100644
index 00000000000..562fb7c4e6c
--- /dev/null
+++ b/modules/nf-core/motus/preplong/main.nf
@@ -0,0 +1,54 @@
+process MOTUS_PREPLONG {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.1.0--pyhdfd78af_0':
+        'biocontainers/motus:3.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*.gz"),  emit: out
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def refdb = db ? "-db ${db}" : ""
+
+    """
+    motus \\
+        prep_long \\
+        $args \\
+        -i $reads \\
+        $refdb \\
+        -t $task.cpus \\
+        -o ${prefix}.gz \\
+        2> >(tee ${prefix}.log >&2)
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
new file mode 100644
index 00000000000..81c339f76b9
--- /dev/null
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -0,0 +1,46 @@
+name: "motus_preplong"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+    description: "Marker gene-based OTU (mOTU) profiling"
+    homepage: "https://motu-tool.org/"
+    documentation: "https://github.com/motu-tool/mOTUs/wiki"
+    tool_dev_url: "https://github.com/motu-tool/mOTUs"
+    doi: "10.1186/s40168-022-01410-z"
+    licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - reads:
+      type: file
+      description:  Long read file to convert, can be fasta(.gz) or fastq(.gz)
+      pattern: "*.{gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - bam:
+      type: file
+      description: FILE converted file (gzipped), ready to be used by motus profile
+      pattern: "*.{gz}"
+
+authors:
+  - "@sofstam"
+maintainers:
+  - "@sofstam"
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
new file mode 100644
index 00000000000..8f2fffe8373
--- /dev/null
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test
@@ -0,0 +1,76 @@
+nextflow_process {
+
+    name "Test Process MOTUS_PREPLONG"
+    script "../main.nf"
+    process "MOTUS_PREPLONG"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "motus"
+    tag "motus/downloaddb"
+    tag "motus/preplong"
+
+    setup {
+        run("MOTUS_DOWNLOADDB") {
+            script "modules/nf-core/motus/downloaddb/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py')
+                ])
+                """
+            }
+        }
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test2_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test2_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] =  MOTUS_DOWNLOADDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+
+    }
+
+}
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test.snap b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1539e40e411
--- /dev/null
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "/Users/sofia.stamouli/Documents/modules/.nf-test/tests/33735d37d2c92cc1168fc5448f4df7ef/work/17/c87488bff86105e9bd5e57349c2822/test.gz"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "/Users/sofia.stamouli/Documents/modules/.nf-test/tests/33735d37d2c92cc1168fc5448f4df7ef/work/17/c87488bff86105e9bd5e57349c2822/test.gz"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-09-05T15:53:45.674303"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ],
+                "out": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-09-05T15:17:39.778376"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/motus/preplong/tests/tags.yml b/modules/nf-core/motus/preplong/tests/tags.yml
new file mode 100644
index 00000000000..bdaae3b2032
--- /dev/null
+++ b/modules/nf-core/motus/preplong/tests/tags.yml
@@ -0,0 +1,2 @@
+motus/preplong:
+  - "modules/nf-core/motus/preplong/**"

From 1cbee6f268c718912a492007b27eed4b60954425 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Thu, 5 Sep 2024 16:14:11 +0200
Subject: [PATCH 02/22] Prettier

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

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 81c339f76b9..46502c59dc6 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -22,7 +22,7 @@ input:
         e.g. `[ id:'sample1', single_end:false ]`
   - reads:
       type: file
-      description:  Long read file to convert, can be fasta(.gz) or fastq(.gz)
+      description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
       pattern: "*.{gz}"
 
 output:

From b881c2e82061d9dd1202ee15a183ce3da96f743a Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Thu, 5 Sep 2024 16:37:08 +0200
Subject: [PATCH 03/22] Update meta

---
 modules/nf-core/motus/preplong/meta.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 46502c59dc6..f73e144148c 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -35,10 +35,14 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - bam:
+  - out:
       type: file
       description: FILE converted file (gzipped), ready to be used by motus profile
       pattern: "*.{gz}"
+  - db:
+      type: directory
+      description: |
+        mOTUs database downloaded by `motus downloadDB`
 
 authors:
   - "@sofstam"

From cf78dcd01548ab929b211e74044c9e1bc26c5bc3 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:32:58 +0200
Subject: [PATCH 04/22] Update modules/nf-core/motus/preplong/main.nf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/motus/preplong/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
index 562fb7c4e6c..9f8408a1cb2 100644
--- a/modules/nf-core/motus/preplong/main.nf
+++ b/modules/nf-core/motus/preplong/main.nf
@@ -12,8 +12,8 @@ process MOTUS_PREPLONG {
     path db
 
     output:
-    tuple val(meta), path("*.gz"),  emit: out
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.gz"), emit: out
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From d0bc778ed12636848b3eba6afab5203cd324fb9d Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:33:49 +0200
Subject: [PATCH 05/22] Update modules/nf-core/motus/preplong/main.nf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/motus/preplong/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
index 9f8408a1cb2..afec13c5d1f 100644
--- a/modules/nf-core/motus/preplong/main.nf
+++ b/modules/nf-core/motus/preplong/main.nf
@@ -44,7 +44,7 @@ process MOTUS_PREPLONG {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.gz
+    echo '' | gzip > ${prefix}.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From ddc3cf709ea76f07965f5a6c9496de0ff682eeed Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:34:23 +0200
Subject: [PATCH 06/22] Update
 modules/nf-core/motus/preplong/tests/main.nf.test

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/motus/preplong/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
index 8f2fffe8373..4ef311f2525 100644
--- a/modules/nf-core/motus/preplong/tests/main.nf.test
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test
@@ -31,7 +31,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test2_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
                 ]
                 input[1] =  MOTUS_DOWNLOADDB.out.db
                 """

From 6d6586da1f28285911c14ad609d6e558af8c70b8 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:34:28 +0200
Subject: [PATCH 07/22] Update
 modules/nf-core/motus/preplong/tests/main.nf.test

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/motus/preplong/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
index 4ef311f2525..4db96dda673 100644
--- a/modules/nf-core/motus/preplong/tests/main.nf.test
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test
@@ -56,7 +56,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['nanopore']['test2_fastq_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
                 ]
                 input[1] =  MOTUS_DOWNLOADDB.out.db
                 """

From 5af72e3753f2613f5a1073d7e6668b100092ddff Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:36:57 +0200
Subject: [PATCH 08/22] Update modules/nf-core/motus/preplong/meta.yml

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/motus/preplong/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index f73e144148c..ab2ba21d385 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -37,7 +37,7 @@ output:
       pattern: "versions.yml"
   - out:
       type: file
-      description: FILE converted file (gzipped), ready to be used by motus profile
+      description: converted file (gzipped), ready to be used by motus profile
       pattern: "*.{gz}"
   - db:
       type: directory

From c0c725eefc1b5c69b9e9efc7fe784e8ab61ee48e Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:37:03 +0200
Subject: [PATCH 09/22] Update
 modules/nf-core/motus/preplong/tests/main.nf.test

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/motus/preplong/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
index 4db96dda673..5ad8e7487f1 100644
--- a/modules/nf-core/motus/preplong/tests/main.nf.test
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test
@@ -23,7 +23,6 @@ nextflow_process {
         }
     }
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
     test("sarscov2 - fasta") {
 
         when {

From 9d66e88d0adf1ee8a1f500a4ed5280fdfffc145d Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 6 Sep 2024 16:29:56 +0200
Subject: [PATCH 10/22] Update snap file

---
 modules/nf-core/motus/preplong/environment.yml       |  3 +--
 modules/nf-core/motus/preplong/meta.yml              | 12 ++++++------
 .../nf-core/motus/preplong/tests/main.nf.test.snap   |  8 ++++----
 3 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml
index fa79445404f..9958f0e0c36 100644
--- a/modules/nf-core/motus/preplong/environment.yml
+++ b/modules/nf-core/motus/preplong/environment.yml
@@ -2,6 +2,5 @@ name: "motus_preplong"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "bioconda::motus=3.1.0"
+  - bioconda::motus=3.1.0
diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index ab2ba21d385..9dab2120193 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -7,12 +7,12 @@ keywords:
   - taxonomic profiling
 tools:
   - "motus":
-    description: "Marker gene-based OTU (mOTU) profiling"
-    homepage: "https://motu-tool.org/"
-    documentation: "https://github.com/motu-tool/mOTUs/wiki"
-    tool_dev_url: "https://github.com/motu-tool/mOTUs"
-    doi: "10.1186/s40168-022-01410-z"
-    licence: ["GPL v3"]
+      description: "Marker gene-based OTU (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1186/s40168-022-01410-z"
+      licence: ["GPL v3"]
 
 input:
   - meta:
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test.snap b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
index 1539e40e411..5ed72ec8a9a 100644
--- a/modules/nf-core/motus/preplong/tests/main.nf.test.snap
+++ b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "/Users/sofia.stamouli/Documents/modules/.nf-test/tests/33735d37d2c92cc1168fc5448f4df7ef/work/17/c87488bff86105e9bd5e57349c2822/test.gz"
+                        "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "/Users/sofia.stamouli/Documents/modules/.nf-test/tests/33735d37d2c92cc1168fc5448f4df7ef/work/17/c87488bff86105e9bd5e57349c2822/test.gz"
+                        "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
@@ -32,7 +32,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-09-05T15:53:45.674303"
+        "timestamp": "2024-09-06T16:29:18.602046"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -67,6 +67,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-09-05T15:17:39.778376"
+        "timestamp": "2024-09-06T15:55:48.439664"
     }
 }
\ No newline at end of file

From b4971df976c3e0cbca111685c043f33515f6083d Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 6 Sep 2024 16:36:29 +0200
Subject: [PATCH 11/22] Fix linting

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

diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml
index 9958f0e0c36..b8ef520eaa2 100644
--- a/modules/nf-core/motus/preplong/environment.yml
+++ b/modules/nf-core/motus/preplong/environment.yml
@@ -1,4 +1,3 @@
-name: "motus_preplong"
 channels:
   - conda-forge
   - bioconda

From 98ee2fc9e47fc0ec6b0f8e6b850b9cac36406cf6 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Thu, 12 Sep 2024 15:13:16 +0200
Subject: [PATCH 12/22] Update meta.yml

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

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 9dab2120193..86139df613f 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - taxonomic profiling
 tools:
   - "motus":
-      description: "Marker gene-based OTU (mOTU) profiling"
+      description: "Marker gene-based operational taxonomic unit (mOTU) profiling"
       homepage: "https://motu-tool.org/"
       documentation: "https://github.com/motu-tool/mOTUs/wiki"
       tool_dev_url: "https://github.com/motu-tool/mOTUs"

From aad473d587dd66b955c4a4a648c7efdd32c00965 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Fri, 4 Oct 2024 13:09:27 +0200
Subject: [PATCH 13/22] Update modules/nf-core/motus/preplong/main.nf

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

diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
index afec13c5d1f..93f75cc37d1 100644
--- a/modules/nf-core/motus/preplong/main.nf
+++ b/modules/nf-core/motus/preplong/main.nf
@@ -33,7 +33,6 @@ process MOTUS_PREPLONG {
         -o ${prefix}.gz \\
         2> >(tee ${prefix}.log >&2)
 
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/')

From 3d9fc0e44a1cf550676317a068bdf29c05aa7fdd Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 13:16:03 +0200
Subject: [PATCH 14/22] Fix formatting

---
 modules/nf-core/motus/preplong/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
index 93f75cc37d1..3fffc149648 100644
--- a/modules/nf-core/motus/preplong/main.nf
+++ b/modules/nf-core/motus/preplong/main.nf
@@ -13,7 +13,7 @@ process MOTUS_PREPLONG {
 
     output:
     tuple val(meta), path("*.gz"), emit: out
-    path "versions.yml"               , emit: versions
+    path "versions.yml"          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From 01e3640719f9dbcbc7d6abfad397564699ccfa51 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 13:55:41 +0200
Subject: [PATCH 15/22] Update meta.yaml

---
 modules/nf-core/motus/preplong/meta.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 86139df613f..2119df8b589 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -15,15 +15,15 @@ tools:
       licence: ["GPL v3"]
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  - reads:
-      type: file
-      description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
-      pattern: "*.{gz}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reads:
+        type: file
+        description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
+        pattern: "*.{gz}"
 
 output:
   - meta:

From b4355646fa9004755775d9f60d0e2202ac1bf889 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 14:23:22 +0200
Subject: [PATCH 16/22] Update meta.yml

---
 modules/nf-core/motus/preplong/meta.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 2119df8b589..25892fc090e 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -24,6 +24,11 @@ input:
         type: file
         description: Long read file to convert, can be fasta(.gz) or fastq(.gz)
         pattern: "*.{gz}"
+  - - db:
+        type: directory
+        description: |
+          mOTUs database downloaded by `motus downloadDB`
+          pattern: "db_mOTU/"
 
 output:
   - meta:

From 5926dce5dd9d15524f557cbf8553c3f7578b0e15 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 14:32:10 +0200
Subject: [PATCH 17/22] Update meta.yaml

---
 modules/nf-core/motus/preplong/meta.yml | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 25892fc090e..e81dcf1486c 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -31,19 +31,20 @@ input:
           pattern: "db_mOTU/"
 
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - out:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.{gz}":
       type: file
       description: converted file (gzipped), ready to be used by motus profile
       pattern: "*.{gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
   - db:
       type: directory
       description: |

From 5223764fa9d5188c30f6efa4d21df8055c5882b7 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 14:35:34 +0200
Subject: [PATCH 18/22] Fix formatting for meta.yaml

---
 modules/nf-core/motus/preplong/meta.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index e81dcf1486c..3c9533fd58c 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -32,15 +32,15 @@ input:
 
 output:
   - out:
-    - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-    - "*.{gz}":
-      type: file
-      description: converted file (gzipped), ready to be used by motus profile
-      pattern: "*.{gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.{gz}":
+          type: file
+          description: converted file (gzipped), ready to be used by motus profile
+          pattern: "*.{gz}"
   - versions:
       type: file
       description: File containing software versions

From 260351dc12fa9f82dd3c54c7f3ff85f3fac5f273 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 14:44:44 +0200
Subject: [PATCH 19/22] Try to fix linting

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

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 3c9533fd58c..9764a92b258 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -37,7 +37,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*.{gz}":
+      - "*.gz":
           type: file
           description: converted file (gzipped), ready to be used by motus profile
           pattern: "*.{gz}"

From 809805a2688b57175d8c750dd32ecc84df4a0c61 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 14:47:17 +0200
Subject: [PATCH 20/22] Remove unnecessary output

---
 modules/nf-core/motus/preplong/meta.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 9764a92b258..ac847690550 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -45,10 +45,6 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - db:
-      type: directory
-      description: |
-        mOTUs database downloaded by `motus downloadDB`
 
 authors:
   - "@sofstam"

From 1dd0666d4526ac6a9ad7b6bf49c24c8e36f83032 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 14:53:37 +0200
Subject: [PATCH 21/22] Fix linting

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

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index ac847690550..22d58794f8c 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -40,7 +40,7 @@ output:
       - "*.gz":
           type: file
           description: converted file (gzipped), ready to be used by motus profile
-          pattern: "*.{gz}"
+          pattern: "*.gz"
   - versions:
       type: file
       description: File containing software versions

From c5cb81e5ccfa05281a2baddc3652f566db9ad989 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <sofia.stamouli@scilifelab.se>
Date: Fri, 4 Oct 2024 15:01:36 +0200
Subject: [PATCH 22/22] Update meta.yml with version.yml

---
 modules/nf-core/motus/preplong/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
index 22d58794f8c..6ef63949a04 100644
--- a/modules/nf-core/motus/preplong/meta.yml
+++ b/modules/nf-core/motus/preplong/meta.yml
@@ -29,7 +29,6 @@ input:
         description: |
           mOTUs database downloaded by `motus downloadDB`
           pattern: "db_mOTU/"
-
 output:
   - out:
       - meta:
@@ -42,9 +41,10 @@ output:
           description: converted file (gzipped), ready to be used by motus profile
           pattern: "*.gz"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
 
 authors:
   - "@sofstam"