Adding Minimac4 to phaseimpute

CHANGELOG.md

@@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#175](https://github.com/nf-core/phaseimpute/pull/175) - Add support for all input files in `.json` or `.yaml` format.
 - [#181](https://github.com/nf-core/phaseimpute/pull/181) - Add nf-co2footprint plugin to the config file.
 - [#184](https://github.com/nf-core/phaseimpute/pull/184) - Add support `.csi` index for `.bam` files.
-- [#188](https://github.com/nf-core/phaseimpute/pull/188) - Add documentation for all subworkflows.
+- [#188](https://github.com/nf-core/phaseimpute/pull/188) - Add documentation for all subworkflows
+- [#204](https://github.com/nf-core/phaseimpute/pull/204) - Add MINIMAC4 support for genotype imputation.
 
 ### `Changed`
 
@@ -127,6 +128,8 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Improve documentation writing
 - [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names (add post-processing for clean up `FILTER_CHR_DWN`, `FILTER_CHR_INP`, `GAWK_ERROR_SPL`, `GAWK_RSQUARE_SPL`). Fix output panel `publishDir`. Fix java version to `17` in `ci.yml` due to new nextflow version.
 
+
+
 ### `Dependencies`
 
 | Dependency    | New version |
@@ -143,6 +146,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 | `r-stitch`    | 1.6.10      |
 | `samtools`    | 1.21        |
 | `shapeit5`    | 1.0.0       |
+| `minimac4`    | 4.1.6       |    
 | `tabix`       | 1.11        |
 | `vcflib`      | 1.0.3       |
 
@@ -159,3 +163,5 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 [Hemanoel Passarelli](https://github.com/hemanoel)
 [Matthias Hörtenhuber](https://github.com/mashehu)
 [Sofia Stamouli](https://github.com/sofstam)
+[Gaspard Ichas](https://github.com/gichas)
+

README.md

@@ -41,7 +41,8 @@ The whole pipeline consists of five main steps, each of which can be run separat
    - **Position Extraction** for targeted imputation sites.
 
 4. **Imputation (`--impute`)**: This is the primary step, where genotypes in the target dataset are imputed using the prepared reference panel. The main steps are:
-   - **Imputation** of the target dataset using tools like [Glimpse1](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html), [Glimpse2](https://odelaneau.github.io/GLIMPSE/), [Stitch](https://github.com/rwdavies/stitch), or [Quilt](https://github.com/rwdavies/QUILT).
+
+   - **Imputation** of the target dataset using tools like [Glimpse1](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html), [Glimpse2](https://odelaneau.github.io/GLIMPSE/), [Stitch](https://github.com/rwdavies/stitch), [Quilt](https://github.com/rwdavies/QUILT) or [Minimac4](https://github.com/statgen/Minimac4).
    - **Ligation** of imputed chunks to produce a final VCF file per sample, with all chromosomes unified.
 
 5. **Validation (`--validate`)**: Assesses imputation accuracy by comparing the imputed dataset to a truth dataset. This step leverages the [Glimpse2](https://odelaneau.github.io/GLIMPSE/) concordance process to summarize differences between two VCF files.

conf/steps/imputation_minimac4.config

@@ -0,0 +1,50 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_MINIMAC4:.*' {
+        publishDir = [enabled: false]
+        tag = { "${meta.id} ${meta.chr}" }
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_MINIMAC4:MINIMAC4_COMPRESSREF' {
+        ext.args   = ''
+        ext.prefix = { "${meta.id}.${meta.chr}.minimac4" }
+        publishDir = [enabled: false]
+        tag = { "${meta.id} ${meta.chr}" }
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_MINIMAC4:MINIMAC4_IMPUTE' {
+        ext.args   = { "--output-format vcf.gz" }
+        ext.prefix = { "${meta.id}.${meta.chr}.minimac4" }
+        tag = { "${meta.id} ${meta.chr}" }
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_MINIMAC4:BCFTOOLS_INDEX' {
+        ext.args   = ''
+        publishDir = [enabled: false]
+        tag = { "${meta.id} ${meta.chr}" }
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_MINIMAC4:.*' {
+        publishDir = [
+            path: { "${params.outdir}/imputation/minimac4/concat" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_MINIMAC4:BCFTOOLS_CONCAT' {
+        ext.args   = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ')
+        ext.prefix = { "${meta.id}.minimac4" }
+    }
+}

conf/test_all.config

@@ -1,75 +1,75 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/phaseimpute -profile test_all,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '4.GB',
-        time: '1.h'
-    ]
-}
-
-params {
-    config_profile_name        = 'Test simulation / imputation / validation mode'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
-
-    // Input data
-    input        = "${projectDir}/tests/csv/sample_sim.csv"
-    input_region = "${projectDir}/tests/csv/region.csv"
-    depth        = 1
-
-    // Genome references
-    fasta        = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz"
-
-    // Panel preparation
-    panel        = "${projectDir}/tests/csv/panel.csv"
-    phase        = true
-    normalize    = true
-    compute_freq = true
-    chunk_model  = "recursive"
-    remove_samples = "NA12878,NA12891,NA12892"
-
-    // Pipeline steps
-    steps = "all"
-
-    // Impute tools
-    tools = "glimpse1,glimpse2,stitch,quilt"
-}
-
-process {
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' {
-        ext.args = ["--window-size 10000", "--window-count 400", "--buffer-size 5000", "--buffer-count 30"].join(' ')
-        ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" }
-        publishDir = [
-            path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: true
-        ]
-    }
-
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' {
-        ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
-        ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
-        publishDir = [
-            path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: true
-        ]
-    }
-
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:GLIMPSE2_CHUNK' {
-        ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
-        ext.prefix = { "${meta.id}_chunks" }
-    }
-}
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/phaseimpute -profile test_all,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '4.GB',
+        time: '1.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test simulation / imputation / validation mode'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input        = "${projectDir}/tests/csv/sample_sim.csv"
+    input_region = "${projectDir}/tests/csv/region.csv"
+    depth        = 1
+
+    // Genome references
+    fasta        = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz"
+
+    // Panel preparation
+    panel        = "${projectDir}/tests/csv/panel.csv"
+    phase        = true
+    normalize    = true
+    compute_freq = true
+    chunk_model  = "recursive"
+    remove_samples = "NA12878,NA12891,NA12892"
+
+    // Pipeline steps
+    steps = "all"
+
+    // Impute tools
+    tools = "glimpse1,glimpse2,stitch,quilt"
+}
+
+process {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' {
+        ext.args = ["--window-size 10000", "--window-count 400", "--buffer-size 5000", "--buffer-count 30"].join(' ')
+        ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" }
+        publishDir = [
+            path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: true
+        ]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' {
+        ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
+        ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
+        publishDir = [
+            path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: true
+        ]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:GLIMPSE2_CHUNK' {
+        ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
+        ext.prefix = { "${meta.id}_chunks" }
+    }
+}

conf/test_all_fullchr.config

@@ -1,40 +1,40 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/phaseimpute -profile test_all_fullchr,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-process {
-    resourceLimits = [
-        cpus: 24,
-        memory: '50.GB',
-        time: '4.h'
-    ]
-}
-
-params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check all steps on full chromosomes'
-
-    // Genome references
-    fasta  = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz"
-    panel  = "${projectDir}/tests/csv/panel_fullchr.csv"
-    input  = "${projectDir}/tests/csv/sample_sim_full.csv"
-
-    // Pipeline steps
-    steps   = "all"
-    tools   = "glimpse1,glimpse2,quilt,stitch"
-    depth   = 1
-
-    // Panelprep optional args
-    remove_samples = "NA12878,NA19401,NA20359,NA12891,NA12892,NA20362"
-    normalize      = true
-    compute_freq   = false
-    phase          = false
-}
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/phaseimpute -profile test_all_fullchr,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 24,
+        memory: '50.GB',
+        time: '4.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check all steps on full chromosomes'
+
+    // Genome references
+    fasta  = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz"
+    panel  = "${projectDir}/tests/csv/panel_fullchr.csv"
+    input  = "${projectDir}/tests/csv/sample_sim_full.csv"
+
+    // Pipeline steps
+    steps   = "all"
+    tools   = "glimpse1,glimpse2,quilt,stitch"
+    depth   = 1
+
+    // Panelprep optional args
+    remove_samples = "NA12878,NA19401,NA20359,NA12891,NA12892,NA20362"
+    normalize      = true
+    compute_freq   = false
+    phase          = false
+}