Make BAM_REGION optional

CHANGELOG.md

@@ -30,6 +30,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#56](https://github.com/nf-core/phaseimpute/pull/56) - Move to nf-test to check the output files names generated. Fix validation and concatenation by chromosomes missing. Add dedicated GLIMPSE1 subworkflow. Fix posfile generation to be done once for glimpse and stitch.
 - [#68](https://github.com/nf-core/phaseimpute/pull/68) - QUILT can handle external params chunks and hap-legend files.
 - [#78](https://github.com/nf-core/phaseimpute/pull/78) - Separate validate step from panel preparation.
+- [#84](https://github.com/nf-core/phaseimpute/pull/84) - Change depth computation to use SAMTOOLS_DEPTH and make separation by chromosome in simulation optional with `--sim_by_reg` parameter.
 
 ### `Fixed`
 

conf/steps/simulation.config

@@ -24,25 +24,42 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_COVERAGE' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_DEPTH' {
+        publishDir = [enabled: false]
+        ext.prefix = { "${meta.id}_C${meta.chr ?: "all"}.stats" }
+    }
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_VIEW' {
+        ext.prefix = { params.sim_by_reg ?
+            "${meta.id}_D${meta.depth}_C${meta.chr ?: "all"}" :
+            "${meta.id}"
+        }
         publishDir = [
-            path: { "${params.outdir}/simulation/stats/" },
+            path: { "${params.outdir}/simulation/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            saveAs: {  params.sim_by_reg ? null : it  }
         ]
-        ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.stats" }
-    }
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_VIEW' {
-        ext.prefix = { "${meta.id}_D${meta.depth}_R${meta.region.replace(':','_')}" }
-        publishDir = [ enabled: false ]
     }
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_INDEX_1' {
-        publishDir = [ enabled: false ]
+        publishDir = [
+            path: { "${params.outdir}/simulation/" },
+            mode: params.publish_dir_mode,
+            saveAs: {  params.sim_by_reg ? null : it  }
+        ]
     }
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_MERGE' {
         ext.prefix = { "${meta.id}" }
     }
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE:SAMTOOLS_INDEX_2' {
         ext.args = ""
     }
+
+    // Coverage process
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_TRT' {
+        ext.prefix = { "${meta.id}_truth" }
+        publishDir = [ enabled: false ]
+    }
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_SIM' {
+        ext.prefix = { "${meta.id}" }
+        publishDir = [ enabled: false ]
+    }
 }

modules.json

@@ -128,10 +128,16 @@
                     },
                     "samtools/coverage": {
                         "branch": "master",
-                        "git_sha": "38afbe42f7db7f19c7a89607c0a71c68f3be3131",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
                     },
+                    "samtools/depth": {
+                        "branch": "master",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/depth/samtools-depth.diff"
+                    },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "f153f1f10e1083c49935565844cccb7453021682",

nextflow.config

@@ -42,6 +42,7 @@ params {
     // Simulate
     depth                       = 1
     genotype                    = null
+    sim_by_reg                  = true
 
     // Validation
     input_truth                 = null

nextflow_schema.json

@@ -84,6 +84,12 @@
                     "default": 1,
                     "fa_icon": "fas fa-list-ol"
                 },
+                "sim_by_reg": {
+                    "type": "boolean",
+                    "description": "Simulate data only for the given region then merge it or simulate all data at once",
+                    "default": true,
+                    "pattern": "true|false"
+                },
                 "genotype": {
                     "type": "string",
                     "description": "Genotype position to use to simulate the data",