Move to nf-core sbwf BEAGLE5

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#226](https://github.com/nf-core/phaseimpute/pull/226) - Remove `BEDTOOLS` and update automated methods description.
 - [#239](https://github.com/nf-core/phaseimpute/pull/239) - Move from local to nf-core sbwf for `STITCH` imputation. Set `--chunks` as optional argument. Update `usage.md`.
 - [#240](https://github.com/nf-core/phaseimpute/pull/240) - Move from local to nf-core sbwf for `GLIMPSE2` imputation. Update `usage.md`.
+- [#243](https://github.com/nf-core/phaseimpute/pull/243) - Move from local to nf-core sbwf for `BEAGLE5` imputation. Update `usage.md`.
 
 ### `Fixed`
 

conf/steps/imputation_beagle5.config

@@ -16,13 +16,7 @@ process {
     // Impute the variants with BEAGLE5
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:.*' {
         publishDir = [ enabled: false ]
-        tag = {"${meta.id} ${meta.chr}"}
-    }
-
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BEAGLE5_BEAGLE' {
-        ext.args = { "gp=true ap=true chrom=${meta.chr}" }
-        ext.prefix = { "${meta.id}.${meta.chr}.beagle5" }
-        publishDir = [ enabled: false ]
+        tag = {"${meta.id} ${meta.regionout ?: meta.chr}"}
     }
 
     // Convert BCF to VCF if necessary
@@ -32,12 +26,31 @@ process {
         publishDir = [ enabled: false ]
     }
 
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BEAGLE5_BEAGLE' {
+        ext.args = { "gp=true ap=true seed=${params.seed}" }
+        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.beagle5" }
+        publishDir = [ enabled: false ]
+    }
+
     // Index the imputed VCF files
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BCFTOOLS_INDEX_BEAGLE' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BCFTOOLS_INDEX_PHASE' {
         ext.args = ''
         publishDir = [ enabled: false ]
     }
 
+    // Ligate all results
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:GLIMPSE2_LIGATE' {
+        ext.args   = { "--seed ${params.seed}" }
+        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.ligate" }
+        publishDir = [ enabled: false ]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_BEAGLE5:BCFTOOLS_INDEX_LIGATE' {
+        ext.args     = "--tbi"
+        publishDir = [ enabled: false ]
+    }
+
     // Concatenate the imputed chromosomes
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_BEAGLE5:.*' {
         publishDir = [

conf/steps/imputation_glimpse2.config

@@ -25,7 +25,7 @@ process {
         publishDir   = [ enabled: false ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:BCFTOOLS_INDEX_1' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:BCFTOOLS_INDEX_PHASE' {
         ext.args     = "--csi"
         publishDir   = [ enabled: false ]
     }
@@ -36,7 +36,7 @@ process {
         publishDir = [ enabled: false ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:BCFTOOLS_INDEX_2' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:BCFTOOLS_INDEX_LIGATE' {
         ext.args     = "--tbi"
         publishDir = [ enabled: false ]
     }

docs/usage.md

@@ -449,7 +449,7 @@ Optionnaly you can provide the following flags:
 | `GLIMPSE2` | ✅                  | ✅ ¹         | ✅                         | ✅           | ❌             | ✅         | ✅            |
 | `QUILT`    | ✅                  | ✅ ²         | ✅                         | ❌           | ✅ ⁴           | ❌⁶        | ✅            |
 | `STITCH`   | ✅                  | ✅ ²         | ✅                         | ❌           | ✅ ³           | ✅         | ✅            |
-| `BEAGLE5`  | ✅                  | ✅ ¹         | ✅                         | ✅           | ❌             | ❌⁶        | ❌⁶           |
+| `BEAGLE5`  | ✅                  | ✅ ¹         | ✅                         | ✅           | ❌             | ✅         | ✅            |
 | `MINIMAC4` | ✅                  | ✅ ¹         | ✅                         | ✅           | ✅ ⁵           | ❌⁶        | ❌⁶           |
 
 > ¹ Alignment files as well as variant calling format (i.e. BAM, CRAM, VCF or BCF)
@@ -661,6 +661,13 @@ nextflow run nf-core/phaseimpute \
 
 The CSV file provided in `--panel` must be prepared with `--steps panelprep` and must contain four columns [panel, chr, vcf, index].
 
+You can optionally provide chunks to parallelize the imputation process using `--chunks`.
+If not provided the full region per chromosome will be used.
+See [Chunks section](#samplesheet-chunks) for more information.
+
+Genetic map can also be provided for better accuracy.
+See [Map section](#samplesheet-map) for more information.
+
 ### MINIMAC4
 
 [MINIMAC4](https://github.com/statgen/Minimac4) is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased haplotypes and can handle very large reference panels.

modules.json

@@ -24,7 +24,12 @@
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["bam_impute_stitch", "bam_vcf_impute_glimpse2", "modules"]
+                        "installed_by": [
+                            "bam_impute_stitch",
+                            "bam_vcf_impute_glimpse2",
+                            "modules",
+                            "vcf_impute_beagle5"
+                        ]
                     },
                     "bcftools/merge": {
                         "branch": "master",
@@ -62,12 +67,12 @@
                     "bcftools/view": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "vcf_impute_beagle5"]
                     },
                     "beagle5/beagle": {
                         "branch": "master",
-                        "git_sha": "359cfb69d521fcb8b56313e9a6ca9d66036aa921",
-                        "installed_by": ["modules"]
+                        "git_sha": "94a767478097e92dca1386ea623d9dae9edc025a",
+                        "installed_by": ["modules", "vcf_impute_beagle5"]
                     },
                     "gawk": {
                         "branch": "master",
@@ -102,7 +107,12 @@
                     "glimpse2/ligate": {
                         "branch": "master",
                         "git_sha": "94a767478097e92dca1386ea623d9dae9edc025a",
-                        "installed_by": ["bam_impute_stitch", "bam_vcf_impute_glimpse2", "modules"]
+                        "installed_by": [
+                            "bam_impute_stitch",
+                            "bam_vcf_impute_glimpse2",
+                            "modules",
+                            "vcf_impute_beagle5"
+                        ]
                     },
                     "glimpse2/phase": {
                         "branch": "master",
@@ -239,6 +249,11 @@
                         "branch": "master",
                         "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
                         "installed_by": ["subworkflows"]
+                    },
+                    "vcf_impute_beagle5": {
+                        "branch": "master",
+                        "git_sha": "e8db6baba21376a4cf0dfc5ba32224eebf51266c",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }