Gridss

.test/config/config.yaml

@@ -36,6 +36,8 @@ calling:
     activate: true
   freebayes:
     activate: true
+  gridss:
+    activate: true
   # See https://varlociraptor.github.io/docs/calling/#generic-variant-calling
   scenario: config/scenario.yaml
   # See http://snpeff.sourceforge.net/SnpSift.html#filter

README.md

@@ -11,6 +11,7 @@ This workflow detects genomic variants with [Delly](https://github.com/dellytool
 
 * Felix Mölder (@FelixMoelder)
 * Johannes Köster (@johanneskoester)
+* Christopher Schröder (@christopher-schroeder)
 
 ## Usage
 

config/config.yaml

@@ -46,6 +46,8 @@ calling:
     activate: true
   freebayes:
     activate: true
+  gridss:
+    activate: true
   # See https://varlociraptor.github.io/docs/calling/#generic-variant-calling
   scenario: config/scenario.yaml
   filter:

workflow/Snakefile

@@ -20,6 +20,7 @@ include: "rules/tmb.smk"
 include: "rules/vega.smk"
 include: "rules/utils.smk"
 include: "rules/oncoprint.smk"
+include: "rules/gridss.smk"
 
 groups = samples["group"].unique()
 
@@ -30,8 +31,9 @@ if is_activated("oncoprint/stratify"):
 
 rule all:
     input:
+        get_gridss_targets(),
         get_final_output(),
         get_tmb_targets(),
         expand("results/plots/oncoprint/{batch}.{event}.pdf",
-               event=config["calling"]["fdr-control"]["events"],
-               batch=batches)
+                event=config["calling"]["fdr-control"]["events"],
+                batch=batches)

workflow/envs/gridss.yaml

@@ -0,0 +1,12 @@
+channels:
+  - conda-forge
+  - bioconda
+  - r
+dependencies:
+  - samtools=1.1.0
+  - ldc=1.13
+  - sambamba=0.7.1
+  - openjdk=11.0.1
+  - r=3.6.0
+  - bwa=0.7.17
+  - gridss=2.8

workflow/rules/common.smk

@@ -116,6 +116,14 @@ def get_tmb_targets():
         return []
 
 
+def get_gridss_targets():
+    if is_activated("calling/gridss"):
+        return expand("results/gridss_vcf/{group}.vcf",
+                      group=groups)
+    else:
+        return []
+
+
 def get_annotated_bcf(wildcards, group=None):
     if group is None:
         group = wildcards.group