Deepvariant subworkflow (issue #614)

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608)
 - An option to restrict analysis to specific contigs [#644](https://github.com/nf-core/raredisease/pull/644)
 - Fastp and ngsbits output files as input of MultiQC [#647](https://github.com/nf-core/raredisease/pull/647/).
+- Replace DeepVariant process with a subworkflow [#651](https://github.com/nf-core/raredisease/pull/651)
 
 ### `Changed`
 

conf/modules/call_snv_deepvariant.config

@@ -21,11 +21,20 @@ process {
         ext.when = params.variant_caller.equals("deepvariant")
     }
 
-    withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT' {
+    withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT:DEEPVARIANT_MAKEEXAMPLES' {
         ext.args = { [
-            "--model_type=${params.analysis_type.toUpperCase()}",
+            "--channels insert_size",
             meta.sex == "1" ? params.genome == 'GRCh37' ? '--haploid_contigs="X,Y"' : '--haploid_contigs="chrX,chrY"' : ''
         ].join(' ') }
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT:DEEPVARIANT_CALLVARIANTS' {
+        ext.args = { [
+            "--checkpoint /opt/models/${params.analysis_type.toLowerCase()}",
+        ].join(' ') }
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT:DEEPVARIANT_POSTPROCESSVARIANTS' {
         ext.prefix = { "${meta.id}_deepvar" }
     }
 

conf/test_full.config

@@ -34,7 +34,7 @@ process {
     withName: 'MARKDUPLICATES' {
         memory          = { check_max( 90.GB * task.attempt, 'memory' ) }
     }
-    withName: 'DEEPVARIANT' {
+    withName: '.*:DEEPVARIANT:DEEPVARIANT_CALLVARIANTS' {
         cpus            = 24
         memory          = { check_max( 90.GB * task.attempt, 'memory' ) }
     }

docs/usage.md

@@ -560,3 +560,22 @@ plugins {
 ```
 
 This should go in your Nextflow configuration file, specified with `-c <YOURCONFIG>` when running the pipeline.
+
+### Calling variants on the GPU with DeepVariant
+
+To use GPU for variant calling you have to override the container image. The GPU-enabled DeepVariant image is very large, so it's not used by default. You need to identify the DeepVariant version used by raredisease. Then replace the container image of the `DEEPVARIANT_CALLVARIANTS` process with one from Google's Docker Hub, `docker.io/google/deepvariant:X.Y.Z-gpu`, changing "X.Y.Z" to the version.
+
+For singularity / apptainer you can use containerOptions = '--nv' to enable GPU access. For Docker, use the `--gpus` option.
+
+If using a queue system like SLURM, or the Cloud, you usually have to enable certain options to get access to GPUs, e.g. the `queue` directive. If you run locally on a server with a single GPU, you can set `maxForks = 1` to prevent starting simultaneous GPU jobs for different samples.
+
+Configuration example:
+
+```
+    withName:"DEEPVARIANT_CALLVARIANTS" {
+        cpus = 6
+        containerOptions = '--nv'
+        container = 'docker.io/google/deepvariant:1.6.1-gpu'
+        maxForks = 1
+    }
+```

modules.json

@@ -111,10 +111,20 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "deepvariant/rundeepvariant": {
+                    "deepvariant/callvariants": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["deepvariant"]
+                    },
+                    "deepvariant/makeexamples": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["deepvariant"]
+                    },
+                    "deepvariant/postprocessvariants": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["deepvariant"]
                     },
                     "eklipse": {
                         "branch": "master",
@@ -517,6 +527,11 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "deepvariant": {
+                        "branch": "master",
+                        "git_sha": "f1236caa87bac87e75698af65281a795cded208c",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",