Move to nf-core sbwf for GLIMPSE2

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#231](https://github.com/nf-core/phaseimpute/pull/231) - Use "panel_id" instead of "id" in the meta map for the panel.
 - [#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`.
 
 ### `Fixed`
 

conf/steps/imputation_glimpse2.config

@@ -14,13 +14,13 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:.*' {
         publishDir = [ enabled: false ]
-        tag = {"Batch ${meta.batch} ${meta.chr}"}
+        tag = {"Batch ${meta.batch} ${meta.regionout ?: meta.chr }"}
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:GLIMPSE2_PHASE' {
         cache = "lenient"
-        ext.prefix   = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse2" }
-        ext.args     = { "--keep-monomorphic-ref-sites" }
+        ext.prefix   = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.glimpse2" }
+        ext.args     = { "--keep-monomorphic-ref-sites --seed ${params.seed}" }
         ext.suffix   = "bcf"
         publishDir   = [ enabled: false ]
     }
@@ -31,6 +31,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_VCF_IMPUTE_GLIMPSE2:GLIMPSE2_LIGATE' {
+        ext.args   = { "--seed ${params.seed}" }
         ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.ligate" }
         publishDir = [ enabled: false ]
     }

conf/steps/imputation_stitch.config

@@ -28,12 +28,12 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:.*' {
         publishDir = [enabled: false]
-        tag = {"Batch ${meta.batch} ${meta.chr}"}
+        tag = {"Batch ${meta.batch} ${meta.regionout ?: meta.chr}"}
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:STITCH' {
         cache = "lenient"
-        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? '.'+ meta.regionout : meta.chr}.stitch" }
+        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.stitch" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:BCFTOOLS_INDEX_1' {

conf/test_glimpse2.config

@@ -34,6 +34,7 @@ params {
 
     // External params
     chunks  = "${projectDir}/tests/csv/chunks.csv"
+    map = "${projectDir}/tests/csv/map_glimpse.csv"
 
     // Impute tools
     tools  = "glimpse2"

docs/usage.md

@@ -446,7 +446,7 @@ Optionnaly you can provide the following flags:
 |            | `--steps impute`(m) | `--input`(m) | `--genome` or `--fasta`(m) | `--panel`(m) | `--posfile`(m) | `--map`(o) | `--chunks`(o) |
 | ---------- | ------------------- | ------------ | -------------------------- | ------------ | -------------- | ---------- | ------------- |
 | `GLIMPSE1` | ✅                  | ✅ ¹         | ✅                         | ✅           | ✅ ³           | ❌⁶        | ✅            |
-| `GLIMPSE2` | ✅                  | ✅ ¹         | ✅                         | ✅           | ❌             | ❌⁶        | ✅            |
+| `GLIMPSE2` | ✅                  | ✅ ¹         | ✅                         | ✅           | ❌             | ✅         | ✅            |
 | `QUILT`    | ✅                  | ✅ ²         | ✅                         | ❌           | ✅ ⁴           | ❌⁶        | ✅            |
 | `STITCH`   | ✅                  | ✅ ²         | ✅                         | ❌           | ✅ ³           | ✅         | ✅            |
 | `BEAGLE5`  | ✅                  | ✅ ¹         | ✅                         | ✅           | ❌             | ❌⁶        | ❌⁶           |
@@ -635,6 +635,13 @@ nextflow run nf-core/phaseimpute \
 
 Make sure the CSV file with the input panel is the output from `--step panelprep` or has been previously prepared.
 
+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.
+
 ### BEAGLE5
 
 [BEAGLE5](https://faculty.washington.edu/browning/beagle/beagle.html) is a software package for analyzing large-scale genetic

modules.json

@@ -24,7 +24,7 @@
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["bam_impute_stitch", "modules"]
+                        "installed_by": ["bam_impute_stitch", "bam_vcf_impute_glimpse2", "modules"]
                     },
                     "bcftools/merge": {
                         "branch": "master",
@@ -91,23 +91,28 @@
                     },
                     "glimpse2/chunk": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "git_sha": "94a767478097e92dca1386ea623d9dae9edc025a",
+                        "installed_by": ["bam_vcf_impute_glimpse2", "modules"]
                     },
                     "glimpse2/concordance": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "cc45bedccf632f7d21bc81dcced99a6870ff3127",
                         "installed_by": ["modules"]
                     },
                     "glimpse2/ligate": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["bam_impute_stitch", "modules"]
+                        "git_sha": "94a767478097e92dca1386ea623d9dae9edc025a",
+                        "installed_by": ["bam_impute_stitch", "bam_vcf_impute_glimpse2", "modules"]
                     },
                     "glimpse2/phase": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "git_sha": "94a767478097e92dca1386ea623d9dae9edc025a",
+                        "installed_by": ["bam_vcf_impute_glimpse2", "modules"]
+                    },
+                    "glimpse2/splitreference": {
+                        "branch": "master",
+                        "git_sha": "94a767478097e92dca1386ea623d9dae9edc025a",
+                        "installed_by": ["bam_vcf_impute_glimpse2"]
                     },
                     "gunzip": {
                         "branch": "master",
@@ -215,6 +220,11 @@
                         "git_sha": "31a8820de9546d701166413a81ce338f5c244550",
                         "installed_by": ["subworkflows"]
                     },
+                    "bam_vcf_impute_glimpse2": {
+                        "branch": "master",
+                        "git_sha": "e337a1d89f92c31041e46dd1509beadce40cb5bb",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",