From 219299d7fc22a55cd3a07c2122044e7ca24b815f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20B=C3=A4uerle?=
 <45968370+famosab@users.noreply.github.com>
Date: Fri, 29 Nov 2024 14:59:31 +0100
Subject: [PATCH] Add module `muse/call`  (#5630)

* start work on muse/call

* correct command and add snap

* prettier

* exclude conda

* change to bioconda

* update snap

* add conda test

* update meta

* change process label

* add indices and update meta

* update containers and version extraction
---
 modules/nf-core/muse/call/environment.yml     |  5 ++
 modules/nf-core/muse/call/main.nf             | 50 +++++++++++++
 modules/nf-core/muse/call/meta.yml            | 72 +++++++++++++++++++
 modules/nf-core/muse/call/tests/main.nf.test  | 72 +++++++++++++++++++
 .../nf-core/muse/call/tests/main.nf.test.snap | 68 ++++++++++++++++++
 modules/nf-core/muse/call/tests/tags.yml      |  2 +
 6 files changed, 269 insertions(+)
 create mode 100644 modules/nf-core/muse/call/environment.yml
 create mode 100644 modules/nf-core/muse/call/main.nf
 create mode 100644 modules/nf-core/muse/call/meta.yml
 create mode 100644 modules/nf-core/muse/call/tests/main.nf.test
 create mode 100644 modules/nf-core/muse/call/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/muse/call/tests/tags.yml

diff --git a/modules/nf-core/muse/call/environment.yml b/modules/nf-core/muse/call/environment.yml
new file mode 100644
index 00000000000..5bc34c10360
--- /dev/null
+++ b/modules/nf-core/muse/call/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::muse=2.1.2"
diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
new file mode 100644
index 00000000000..b4559761ab0
--- /dev/null
+++ b/modules/nf-core/muse/call/main.nf
@@ -0,0 +1,50 @@
+process MUSE_CALL {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9f/9f0ebb574ef5eed2a6e034f1b2feea6c252d1ab0c8bc5135a669059aa1f4d2ca/data':
+        'community.wave.seqera.io/library/muse:6637291dcbb0bdb8' }"
+
+    input:
+    tuple val(meta), path(tumor_bam), path(tumor_bai), path(normal_bam), path(normal_bai)
+    tuple val(meta2), path(reference)
+
+    output:
+    tuple val(meta), path("*.MuSE.txt"), emit: txt
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    MuSE \\
+        call \\
+        $args \\
+        -f $reference \\
+        -O ${prefix}  \\
+        -n $task.cpus \\
+        $tumor_bam    \\
+        $normal_bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.MuSE.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/muse/call/meta.yml b/modules/nf-core/muse/call/meta.yml
new file mode 100644
index 00000000000..6733677dbdc
--- /dev/null
+++ b/modules/nf-core/muse/call/meta.yml
@@ -0,0 +1,72 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "muse_call"
+description: pre-filtering and calculating position-specific summary statistics using
+  the Markov substitution model
+keywords:
+  - variant calling
+  - somatic
+  - wgs
+  - wxs
+  - vcf
+tools:
+  - "MuSE":
+      description: "Somatic point mutation caller based on Markov substitution model
+        for molecular evolution"
+      homepage: "https://bioinformatics.mdanderson.org/public-software/muse/"
+      documentation: "https://github.com/wwylab/MuSE"
+      tool_dev_url: "https://github.com/wwylab/MuSE"
+      doi: "10.1101/gr.278456.123"
+      licence: ["https://github.com/danielfan/MuSE/blob/master/LICENSE"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - tumor_bam:
+        type: file
+        description: Sorted tumor BAM file
+        pattern: "*.bam"
+    - tumor_bai:
+        type: file
+        description: Index file for the tumor BAM file
+        pattern: "*.bai"
+    - normal_bam:
+        type: file
+        description: Sorted matched normal BAM file
+        pattern: "*.bam"
+    - normal_bai:
+        type: file
+        description: Index file for the normal BAM file
+        pattern: "*.bai"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. `[ id:'test' ]`
+    - reference:
+        type: file
+        description: reference genome file
+        pattern: ".fasta"
+output:
+  - txt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.MuSE.txt":
+          type: file
+          description: position-specific summary statistics
+          pattern: "*.MuSE.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"
diff --git a/modules/nf-core/muse/call/tests/main.nf.test b/modules/nf-core/muse/call/tests/main.nf.test
new file mode 100644
index 00000000000..b5e441ec32d
--- /dev/null
+++ b/modules/nf-core/muse/call/tests/main.nf.test
@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process MUSE_CALL"
+    script "../main.nf"
+    process "MUSE_CALL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "muse"
+    tag "muse/call"
+
+    test("human - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'reference' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/muse/call/tests/main.nf.test.snap b/modules/nf-core/muse/call/tests/main.nf.test.snap
new file mode 100644
index 00000000000..ead8906a9ce
--- /dev/null
+++ b/modules/nf-core/muse/call/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "human - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-29T14:30:48.292828"
+    },
+    "human - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,3a38ee9131a217cc56199bd4a6b18e1d"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,3a38ee9131a217cc56199bd4a6b18e1d"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-29T14:30:32.522553"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/muse/call/tests/tags.yml b/modules/nf-core/muse/call/tests/tags.yml
new file mode 100644
index 00000000000..4e04a91a4af
--- /dev/null
+++ b/modules/nf-core/muse/call/tests/tags.yml
@@ -0,0 +1,2 @@
+muse/call:
+  - "modules/nf-core/muse/call/**"