From 6564c6a2b90e5dcd9597d21a3e5ff8a9b69fff80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 17 May 2024 11:39:48 +0200
Subject: [PATCH 01/11] start work on muse/call

---
 modules/nf-core/muse/Dockerfile               | 17 +++++
 modules/nf-core/muse/README.md                | 17 +++++
 modules/nf-core/muse/call/environment.yml     |  9 +++
 modules/nf-core/muse/call/main.nf             | 63 +++++++++++++++++
 modules/nf-core/muse/call/meta.yml            | 61 +++++++++++++++++
 modules/nf-core/muse/call/tests/main.nf.test  | 68 +++++++++++++++++++
 .../nf-core/muse/call/tests/main.nf.test.snap | 58 ++++++++++++++++
 modules/nf-core/muse/call/tests/tags.yml      |  2 +
 8 files changed, 295 insertions(+)
 create mode 100644 modules/nf-core/muse/Dockerfile
 create mode 100644 modules/nf-core/muse/README.md
 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/Dockerfile b/modules/nf-core/muse/Dockerfile
new file mode 100644
index 00000000000..51c13aa0c05
--- /dev/null
+++ b/modules/nf-core/muse/Dockerfile
@@ -0,0 +1,17 @@
+# Dockerfile to create a container with MuSE v
+
+FROM ubuntu:20.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    git g++ cmake autoconf libtool liblzma-dev zlib1g-dev libbz2-dev libcurl3-dev libssl-dev \
+    ca-certificates cpp make libltdl-dev wget unzip \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN git clone --recursive https://github.com/wwylab/MuSE
+RUN cd MuSE && ./install_muse.sh
+
+RUN mkdir /MuSE/bin
+RUN cp /MuSE/MuSE /MuSE/bin
+RUN PATH=$PATH:/MuSE/bin
diff --git a/modules/nf-core/muse/README.md b/modules/nf-core/muse/README.md
new file mode 100644
index 00000000000..a4830a77381
--- /dev/null
+++ b/modules/nf-core/muse/README.md
@@ -0,0 +1,17 @@
+# Updating the Docker image
+So far no public docker image is available for MuSE. This might change in the future, see Issue [#21](https://github.com/wwylab/MuSE/issues/21) on the official repository. Until then we have to build it ourselves using the provided Dockerfile.
+
+1. Build docker image using provided Dockerfile.
+
+   ```bash
+   docker build -t muse:<VERSION> --platform linux/amd64 .
+   ```
+
+2. Access rights are needed to push the container to the Dockerhub nf-core organization, please ask a core team member to do so.
+
+   ```bash
+   docker tag muse:<VERSION> quay.io/nf-core/muse:<VERSION>
+   docker push quay.io/nf-core/muse:<VERSION>
+   ```
+
+3. Make the image public.
diff --git a/modules/nf-core/muse/call/environment.yml b/modules/nf-core/muse/call/environment.yml
new file mode 100644
index 00000000000..939833dbe60
--- /dev/null
+++ b/modules/nf-core/muse/call/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "muse_call"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::muse=1.0.rc"
diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
new file mode 100644
index 00000000000..44ecf4164e2
--- /dev/null
+++ b/modules/nf-core/muse/call/main.nf
@@ -0,0 +1,63 @@
+process MUSE_CALL {
+    tag "$meta.id"
+    label 'process_high'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    //conda "${moduleDir}/environment.yml"
+    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //     'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+    //     'docker.io/library/muse:2.1' }"
+
+    container "muse:2.1"
+
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "MUSE module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
+    input:
+    tuple val(meta), path(tumor_bam), path(normal_bam)
+    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}"
+    def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    MuSE/MuSE call \\
+        $args \\
+        -f $reference \\
+        -O ${prefix}  \\
+        -n $task.cpus \\
+        $tumor_bam    \\
+        $normal_bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        muse: ${VERSION}
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.MuSE.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        muse: ${VERSION}
+    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..569669d6beb
--- /dev/null
+++ b/modules/nf-core/muse/call/meta.yml
@@ -0,0 +1,61 @@
+---
+# 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:
+  - genomics
+  - 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']
+
+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"
+  - normal_bam:
+      type: file
+      description: Sorted matched normal BAM file
+      pattern: "*.bam"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. `[ id:'test' ]`
+  - reference:
+      type: file
+      description: faidx indexed reference genome file
+      pattern: ".fasta"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - txt:
+      type: file
+      description: position-specific summary statistics
+      pattern: "*.MuSE.txt"
+
+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..c6f53d7e77c
--- /dev/null
+++ b/modules/nf-core/muse/call/tests/main.nf.test
@@ -0,0 +1,68 @@
+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/test.paired_end.recalibrated.sorted.bam', 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/test.paired_end.recalibrated.sorted.bam', 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..38e3c5e2fd9
--- /dev/null
+++ b/modules/nf-core/muse/call/tests/main.nf.test.snap
@@ -0,0 +1,58 @@
+{
+    "human - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-17T10:43:39.296254"
+    },
+    "human - bam": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "txt": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-17T10:43:31.511233"
+    }
+}
\ 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/**"

From 7a17907eebfffa3b08ce48a9f73efbe61b8f73fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 17 May 2024 13:35:35 +0200
Subject: [PATCH 02/11] correct command and add snap

---
 modules/nf-core/muse/call/main.nf             | 12 +++++------
 .../nf-core/muse/call/tests/main.nf.test.snap | 20 ++++++++++++++-----
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index 44ecf4164e2..8528b2c3d41 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -2,16 +2,13 @@ process MUSE_CALL {
     tag "$meta.id"
     label 'process_high'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    //conda "${moduleDir}/environment.yml"
+    // TODO Update when maintainer publishes conda package and container
+    // conda "${moduleDir}/environment.yml"
     // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     //     'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
     //     'docker.io/library/muse:2.1' }"
 
-    container "muse:2.1"
+    container "docker.io/famkebaeuerle/muse:2.1"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
@@ -34,7 +31,8 @@ process MUSE_CALL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
-    MuSE/MuSE call \\
+    /MuSE/MuSE \\
+        call \\
         $args \\
         -f $reference \\
         -O ${prefix}  \\
diff --git a/modules/nf-core/muse/call/tests/main.nf.test.snap b/modules/nf-core/muse/call/tests/main.nf.test.snap
index 38e3c5e2fd9..4dc142c8e80 100644
--- a/modules/nf-core/muse/call/tests/main.nf.test.snap
+++ b/modules/nf-core/muse/call/tests/main.nf.test.snap
@@ -36,16 +36,26 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,5f2f2279cd902f56c85156be77259660"
+                    ]
                 ],
                 "1": [
-                    
+                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
                 ],
                 "txt": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.MuSE.txt:md5,5f2f2279cd902f56c85156be77259660"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
                 ]
             }
         ],
@@ -53,6 +63,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.0"
         },
-        "timestamp": "2024-05-17T10:43:31.511233"
+        "timestamp": "2024-05-17T13:28:05.488472"
     }
 }
\ No newline at end of file

From 4b56b32461f06f93ffc1c594c7914a8a9e115adf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 17 May 2024 16:20:29 +0200
Subject: [PATCH 03/11] prettier

---
 modules/nf-core/muse/README.md     | 1 +
 modules/nf-core/muse/call/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/muse/README.md b/modules/nf-core/muse/README.md
index a4830a77381..0cc74596063 100644
--- a/modules/nf-core/muse/README.md
+++ b/modules/nf-core/muse/README.md
@@ -1,4 +1,5 @@
 # Updating the Docker image
+
 So far no public docker image is available for MuSE. This might change in the future, see Issue [#21](https://github.com/wwylab/MuSE/issues/21) on the official repository. Until then we have to build it ourselves using the provided Dockerfile.
 
 1. Build docker image using provided Dockerfile.
diff --git a/modules/nf-core/muse/call/meta.yml b/modules/nf-core/muse/call/meta.yml
index 569669d6beb..4f62284323b 100644
--- a/modules/nf-core/muse/call/meta.yml
+++ b/modules/nf-core/muse/call/meta.yml
@@ -14,7 +14,7 @@ tools:
       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']
+      licence: ["https://github.com/danielfan/MuSE/blob/master/LICENSE"]
 
 input:
   - meta:

From 60f9acb5312f5966c76d377f537400e6bf2abf11 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 17 May 2024 16:31:20 +0200
Subject: [PATCH 04/11] exclude conda

---
 .github/workflows/test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 43f9fa216ba..c36f2828911 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -607,6 +607,8 @@ jobs:
             path: modules/nf-core/merquryfk/ploidyplot
           - profile: conda
             path: modules/nf-core/molkartgarage/clahe
+          - profile: conda
+            path: modules/nf-core/muse/call
           - profile: conda
             path: modules/nf-core/quartonotebook
           - profile: conda

From 4260160581896cdfd223d5cc1a1e2c353451b9de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 15 Nov 2024 10:34:06 +0100
Subject: [PATCH 05/11] change to bioconda

---
 modules/nf-core/muse/Dockerfile           | 17 --------------
 modules/nf-core/muse/README.md            | 18 ---------------
 modules/nf-core/muse/call/environment.yml |  5 +----
 modules/nf-core/muse/call/main.nf         | 27 ++++++++---------------
 4 files changed, 10 insertions(+), 57 deletions(-)
 delete mode 100644 modules/nf-core/muse/Dockerfile
 delete mode 100644 modules/nf-core/muse/README.md

diff --git a/modules/nf-core/muse/Dockerfile b/modules/nf-core/muse/Dockerfile
deleted file mode 100644
index 51c13aa0c05..00000000000
--- a/modules/nf-core/muse/Dockerfile
+++ /dev/null
@@ -1,17 +0,0 @@
-# Dockerfile to create a container with MuSE v
-
-FROM ubuntu:20.04
-
-ARG DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    git g++ cmake autoconf libtool liblzma-dev zlib1g-dev libbz2-dev libcurl3-dev libssl-dev \
-    ca-certificates cpp make libltdl-dev wget unzip \
-    && apt-get clean && rm -rf /var/lib/apt/lists/*
-
-RUN git clone --recursive https://github.com/wwylab/MuSE
-RUN cd MuSE && ./install_muse.sh
-
-RUN mkdir /MuSE/bin
-RUN cp /MuSE/MuSE /MuSE/bin
-RUN PATH=$PATH:/MuSE/bin
diff --git a/modules/nf-core/muse/README.md b/modules/nf-core/muse/README.md
deleted file mode 100644
index 0cc74596063..00000000000
--- a/modules/nf-core/muse/README.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# Updating the Docker image
-
-So far no public docker image is available for MuSE. This might change in the future, see Issue [#21](https://github.com/wwylab/MuSE/issues/21) on the official repository. Until then we have to build it ourselves using the provided Dockerfile.
-
-1. Build docker image using provided Dockerfile.
-
-   ```bash
-   docker build -t muse:<VERSION> --platform linux/amd64 .
-   ```
-
-2. Access rights are needed to push the container to the Dockerhub nf-core organization, please ask a core team member to do so.
-
-   ```bash
-   docker tag muse:<VERSION> quay.io/nf-core/muse:<VERSION>
-   docker push quay.io/nf-core/muse:<VERSION>
-   ```
-
-3. Make the image public.
diff --git a/modules/nf-core/muse/call/environment.yml b/modules/nf-core/muse/call/environment.yml
index 939833dbe60..38889f25fe4 100644
--- a/modules/nf-core/muse/call/environment.yml
+++ b/modules/nf-core/muse/call/environment.yml
@@ -1,9 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 name: "muse_call"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "bioconda::muse=1.0.rc"
+  - "bioconda::muse=2.1.2"
diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index 8528b2c3d41..7b35770d1da 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -2,18 +2,10 @@ process MUSE_CALL {
     tag "$meta.id"
     label 'process_high'
 
-    // TODO Update when maintainer publishes conda package and container
-    // conda "${moduleDir}/environment.yml"
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-    //     'docker.io/library/muse:2.1' }"
-
-    container "docker.io/famkebaeuerle/muse:2.1"
-
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "MUSE module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/muse_sump:6020175d1ed543c4':
+        'community.wave.seqera.io/library/muse_sump:3847abd544ae3eb6' }"
 
     input:
     tuple val(meta), path(tumor_bam), path(normal_bam)
@@ -29,9 +21,9 @@ process MUSE_CALL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '2.1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
-    /MuSE/MuSE \\
+    MuSE \\
         call \\
         $args \\
         -f $reference \\
@@ -42,20 +34,19 @@ process MUSE_CALL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        muse: ${VERSION}
+        MuSE: ${VERSION}
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '2.1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.MuSE.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        muse: ${VERSION}
+        MuSE: ${VERSION}
     END_VERSIONS
     """
 }

From c03b8c7b999eaf6996f2b1edc5b04c458458ad40 Mon Sep 17 00:00:00 2001
From: famosab <famke.baeuerle@gmail.com>
Date: Fri, 15 Nov 2024 10:52:57 +0100
Subject: [PATCH 06/11] update snap

---
 modules/nf-core/muse/call/environment.yml     |  1 -
 modules/nf-core/muse/call/main.nf             |  4 +-
 modules/nf-core/muse/call/meta.yml            | 80 ++++++++++---------
 .../nf-core/muse/call/tests/main.nf.test.snap | 24 +++---
 4 files changed, 55 insertions(+), 54 deletions(-)

diff --git a/modules/nf-core/muse/call/environment.yml b/modules/nf-core/muse/call/environment.yml
index 38889f25fe4..5bc34c10360 100644
--- a/modules/nf-core/muse/call/environment.yml
+++ b/modules/nf-core/muse/call/environment.yml
@@ -1,4 +1,3 @@
-name: "muse_call"
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index 7b35770d1da..91f96f5c51e 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -4,8 +4,8 @@ process MUSE_CALL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/muse_sump:6020175d1ed543c4':
-        'community.wave.seqera.io/library/muse_sump:3847abd544ae3eb6' }"
+        'oras://community.wave.seqera.io/library/muse:2.1.2--f6ec9e78771509ff':
+        'community.wave.seqera.io/library/muse:2.1.2--e8279641c6ef8c63' }"
 
     input:
     tuple val(meta), path(tumor_bam), path(normal_bam)
diff --git a/modules/nf-core/muse/call/meta.yml b/modules/nf-core/muse/call/meta.yml
index 4f62284323b..f582421d171 100644
--- a/modules/nf-core/muse/call/meta.yml
+++ b/modules/nf-core/muse/call/meta.yml
@@ -1,7 +1,7 @@
----
 # 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
+description: pre-filtering and calculating position-specific summary statistics using
+  the Markov substitution model
 keywords:
   - genomics
   - wgs
@@ -9,52 +9,54 @@ keywords:
   - vcf
 tools:
   - "MuSE":
-      description: "Somatic point mutation caller based on Markov substitution model for molecular evolution"
+      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"
-  - normal_bam:
-      type: file
-      description: Sorted matched normal BAM file
-      pattern: "*.bam"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information.
-        e.g. `[ id:'test' ]`
-  - reference:
-      type: file
-      description: faidx indexed reference genome file
-      pattern: ".fasta"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - tumor_bam:
+        type: file
+        description: Sorted tumor BAM file
+        pattern: "*.bam"
+    - normal_bam:
+        type: file
+        description: Sorted matched normal BAM file
+        pattern: "*.bam"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. `[ id:'test' ]`
+    - reference:
+        type: file
+        description: faidx indexed reference genome file
+        pattern: ".fasta"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1' ]`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - txt:
-      type: file
-      description: position-specific summary statistics
-      pattern: "*.MuSE.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:
diff --git a/modules/nf-core/muse/call/tests/main.nf.test.snap b/modules/nf-core/muse/call/tests/main.nf.test.snap
index 4dc142c8e80..d698dad3a74 100644
--- a/modules/nf-core/muse/call/tests/main.nf.test.snap
+++ b/modules/nf-core/muse/call/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
+                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
                 ],
                 "txt": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
+                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-17T10:43:39.296254"
+        "timestamp": "2024-11-15T10:51:43.352355237"
     },
     "human - bam": {
         "content": [
@@ -40,29 +40,29 @@
                         {
                             "id": "test"
                         },
-                        "test.MuSE.txt:md5,5f2f2279cd902f56c85156be77259660"
+                        "test.MuSE.txt:md5,639e250d6b7621286c1563b9244f2645"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
+                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
                 ],
                 "txt": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.MuSE.txt:md5,5f2f2279cd902f56c85156be77259660"
+                        "test.MuSE.txt:md5,639e250d6b7621286c1563b9244f2645"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c863d3ffccbea6b9229b91017f5935ff"
+                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-17T13:28:05.488472"
+        "timestamp": "2024-11-15T10:51:35.004030902"
     }
 }
\ No newline at end of file

From 8a78b9a4be4dd9fbf902202e87f539e1a4a066aa Mon Sep 17 00:00:00 2001
From: famosab <famke.baeuerle@gmail.com>
Date: Fri, 15 Nov 2024 10:57:35 +0100
Subject: [PATCH 07/11] add conda test

---
 .github/workflows/test.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3bc1981e6e2..43fe9733d3a 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -610,8 +610,6 @@ jobs:
             path: modules/nf-core/merquryfk/ploidyplot
           - profile: conda
             path: modules/nf-core/molkartgarage/clahe
-          - profile: conda
-            path: modules/nf-core/muse/call
           - profile: conda
             path: modules/nf-core/quartonotebook
           - profile: conda

From 951bc523bf58b1dee289c8166da780f46fcbb360 Mon Sep 17 00:00:00 2001
From: famosab <famke.baeuerle@gmail.com>
Date: Fri, 15 Nov 2024 13:17:36 +0100
Subject: [PATCH 08/11] update meta

---
 modules/nf-core/muse/call/meta.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/muse/call/meta.yml b/modules/nf-core/muse/call/meta.yml
index f582421d171..b1b7bec3df3 100644
--- a/modules/nf-core/muse/call/meta.yml
+++ b/modules/nf-core/muse/call/meta.yml
@@ -3,7 +3,8 @@ name: "muse_call"
 description: pre-filtering and calculating position-specific summary statistics using
   the Markov substitution model
 keywords:
-  - genomics
+  - variant calling
+  - somatic
   - wgs
   - wxs
   - vcf

From 6600c946fcc3101a56f32c04a6089bf6244fe4cc Mon Sep 17 00:00:00 2001
From: famosab <famke.baeuerle@gmail.com>
Date: Fri, 15 Nov 2024 13:22:26 +0100
Subject: [PATCH 09/11] change process label

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

diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index 91f96f5c51e..bae02808d76 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -1,6 +1,6 @@
 process MUSE_CALL {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

From f3fe172819023744ed5f1beffd2fd14dfef3418d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 29 Nov 2024 14:14:14 +0100
Subject: [PATCH 10/11] add indices and update meta

---
 modules/nf-core/muse/call/main.nf            |  2 +-
 modules/nf-core/muse/call/meta.yml           | 10 +++++++++-
 modules/nf-core/muse/call/tests/main.nf.test |  8 ++++++--
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index bae02808d76..4a856a695bc 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -8,7 +8,7 @@ process MUSE_CALL {
         'community.wave.seqera.io/library/muse:2.1.2--e8279641c6ef8c63' }"
 
     input:
-    tuple val(meta), path(tumor_bam), path(normal_bam)
+    tuple val(meta), path(tumor_bam), path(tumor_bai), path(normal_bam), path(normal_bai)
     tuple val(meta2), path(reference)
 
     output:
diff --git a/modules/nf-core/muse/call/meta.yml b/modules/nf-core/muse/call/meta.yml
index b1b7bec3df3..6733677dbdc 100644
--- a/modules/nf-core/muse/call/meta.yml
+++ b/modules/nf-core/muse/call/meta.yml
@@ -29,10 +29,18 @@ input:
         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: |
@@ -40,7 +48,7 @@ input:
           e.g. `[ id:'test' ]`
     - reference:
         type: file
-        description: faidx indexed reference genome file
+        description: reference genome file
         pattern: ".fasta"
 output:
   - txt:
diff --git a/modules/nf-core/muse/call/tests/main.nf.test b/modules/nf-core/muse/call/tests/main.nf.test
index c6f53d7e77c..b5e441ec32d 100644
--- a/modules/nf-core/muse/call/tests/main.nf.test
+++ b/modules/nf-core/muse/call/tests/main.nf.test
@@ -17,7 +17,9 @@ nextflow_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/test.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
@@ -46,7 +48,9 @@ nextflow_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/test.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

From 3243d1cc999f600b7a7e09e20abef8716374ea77 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Fri, 29 Nov 2024 14:31:53 +0100
Subject: [PATCH 11/11] update containers and version extraction

---
 modules/nf-core/muse/call/main.nf                | 10 ++++------
 .../nf-core/muse/call/tests/main.nf.test.snap    | 16 ++++++++--------
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/muse/call/main.nf b/modules/nf-core/muse/call/main.nf
index 4a856a695bc..b4559761ab0 100644
--- a/modules/nf-core/muse/call/main.nf
+++ b/modules/nf-core/muse/call/main.nf
@@ -4,8 +4,8 @@ process MUSE_CALL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/muse:2.1.2--f6ec9e78771509ff':
-        'community.wave.seqera.io/library/muse:2.1.2--e8279641c6ef8c63' }"
+        '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)
@@ -21,7 +21,6 @@ process MUSE_CALL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     MuSE \\
         call \\
@@ -34,19 +33,18 @@ process MUSE_CALL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        MuSE: ${VERSION}
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" )
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.MuSE.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        MuSE: ${VERSION}
+        MuSE: \$( MuSE --version | sed -e "s/MuSE, version //g" )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/muse/call/tests/main.nf.test.snap b/modules/nf-core/muse/call/tests/main.nf.test.snap
index d698dad3a74..ead8906a9ce 100644
--- a/modules/nf-core/muse/call/tests/main.nf.test.snap
+++ b/modules/nf-core/muse/call/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
                 ],
                 "txt": [
                     [
@@ -22,7 +22,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
                 ]
             }
         ],
@@ -30,7 +30,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-15T10:51:43.352355237"
+        "timestamp": "2024-11-29T14:30:48.292828"
     },
     "human - bam": {
         "content": [
@@ -40,22 +40,22 @@
                         {
                             "id": "test"
                         },
-                        "test.MuSE.txt:md5,639e250d6b7621286c1563b9244f2645"
+                        "test.MuSE.txt:md5,3a38ee9131a217cc56199bd4a6b18e1d"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
                 ],
                 "txt": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.MuSE.txt:md5,639e250d6b7621286c1563b9244f2645"
+                        "test.MuSE.txt:md5,3a38ee9131a217cc56199bd4a6b18e1d"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,182c20f31394d1d406428dab96ec3b3e"
+                    "versions.yml:md5,de7c8f535f5b17473ed6aab68f1d70c1"
                 ]
             }
         ],
@@ -63,6 +63,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-15T10:51:35.004030902"
+        "timestamp": "2024-11-29T14:30:32.522553"
     }
 }
\ No newline at end of file