feat: add MuSE as new somatic variant caller

CHANGELOG.md

@@ -42,6 +42,7 @@ A set of connecting glaciers.
 - [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update
 - [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair
 - [1730](https://github.com/nf-core/sarek/pull/1730) - Enable Harshil Alignment™️ in VS Code workspace settings
+- [1744](https://github.com/nf-core/sarek/pull/1744) - Add MuSE as new somatic variant caller
 
 ### Changed
 
@@ -100,6 +101,7 @@ A set of connecting glaciers.
 | `samtools`    | 1.20        | 1.21        |
 | `sentieon`    | 202308.02   | 202308.03   |
 | `svdb`        | 2.8.1       | 2.8.2       |
+| `MuSE`        |             | 2.1.2       |
 
 ### Parameters
 

CITATIONS.md

@@ -150,6 +150,10 @@
 
   > Wilm et al. LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012; 40(22):11189-201.
 
+- [MuSE](https://pubmed.ncbi.nlm.nih.gov/38589250/)
+
+  > Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. Genome Res. 2024 May 15;34(4):633-641. doi: 10.1101/gr.278456.123. PMID: 38589250; PMCID: PMC11146589.
+
 ## R packages
 
 - [R](https://www.R-project.org/)

README.md

@@ -62,6 +62,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
   - `Strelka2`
   - `TIDDIT`
   - `Lofreq`
+  - `MuSE`
 - Variant filtering and annotation (`SnpEff`, `Ensembl VEP`, `BCFtools annotate`)
 - Summarise and represent QC (`MultiQC`)
 

conf/modules/muse.config

@@ -0,0 +1,37 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+// MUSE
+
+process {
+
+    withName: 'MUSE_SUMP' {
+        ext.args   = { params.wes ? '-E' : '-G' }
+        ext.when   = { params.tools && params.tools.contains('muse') }
+        ext.prefix = { "${meta.id}.muse" }
+        publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/muse/${meta.id}/" },
+                pattern: "*{vcf.gz,vcf.gz.tbi}",
+            ]
+    }
+
+    withName: 'CRAM_TO_BAM_TUMOR' {
+        ext.prefix = {"${meta.tumor_id}"}
+    }
+
+    withName: 'CRAM_TO_BAM_NORMAL' {
+        ext.prefix = {"${meta.normal_id}"}
+    }
+
+}

conf/test_full.config

@@ -18,7 +18,7 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'
 
     // Other params
-    tools       = 'ngscheckmate,lofreq,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
+    tools       = 'ngscheckmate,lofreq,strelka,mutect2,muse,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
     split_fastq = 20000000
     intervals   = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
     wes         = true

docs/output.md

@@ -44,6 +44,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [Sentieon Haplotyper joint germline variant calling](#sentieon-haplotyper-joint-germline-variant-calling)
     - [Strelka](#strelka)
     - [Lofreq](#lofreq)
+    - [MuSE](#muse)
   - [Structural Variants](#structural-variants)
     - [Indexcov](#indexcov)
     - [Manta](#manta)
@@ -591,6 +592,20 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 
   </details>
 
+#### MuSE
+
+[MuSE](https://github.com/wwylab/MuSE) is an accurate and ultra-fast somatic mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples. This tool is unique in accounting for tumor heterogeneity using a sample-specific error model that improves sensitivity and specificity in mutation calling from sequencing data. For further reading see the [recently published paper](https://genome.cshlp.org/content/early/2024/05/03/gr.278456.123.long).
+
+<details markdown = "1">
+<summary>Output files for tumor-normal samples</summary>
+
+**Output directory: `{outdir}/variant_calling/muse/<tumorsample_vs_normalsample>/`**
+
+-`<tumorsample_vs_normalsample>.vcf.gz`
+-VCF with called variants. Fields are named TUMOR and NORMAL.
+
+</details>
+
 ### Structural Variants
 
 #### indexcov

docs/usage.md

@@ -583,7 +583,8 @@ This list is by no means exhaustive and it will depend on the specific analysis
 | [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)                 |  x  |  x  |   x    |     -     |     x      |           x            |
 | [lofreq](https://github.com/CSB5/lofreq)                                                                |  x  |  x  |   x    |     -     |     x      |           -            |
 | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |     x     |     x      |           -            |
-| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |     x     |     -      |           x            |
+| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   -    |     -     |     -      |           x            |
+| [MuSE](https://github.com/wwylab/MuSE)                                                                  |  x  |  x  |   x    |     -     |     -      |           x            |
 | [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |     x     |     x      |           x            |
 | [indexcov](https://github.com/brentp/goleft/tree/master/indexcov)                                       |  x  |  -  |   -    |     x     |     -      |           x            |
 | [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |     x     |     x      |           x            |

modules.json

@@ -355,6 +355,16 @@
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
+                    "muse/call": {
+                        "branch": "master",
+                        "git_sha": "219299d7fc22a55cd3a07c2122044e7ca24b815f",
+                        "installed_by": ["modules"]
+                    },
+                    "muse/sump": {
+                        "branch": "master",
+                        "git_sha": "8e17f287034692420127d807c7631ae5ca4b9d0c",
+                        "installed_by": ["modules"]
+                    },
                     "ngscheckmate/ncm": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",