Merge pull request #637 from broadinstitute/hm-add-kraken-rule

Add metagenomics rule to run only kraken
broadinstitute · Jun 27, 2017 · 6c63009 · 6c63009
2 parents 123401f + b252588
commit 6c63009
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/pipes/rules/metagenomics.rules b/pipes/rules/metagenomics.rules
@@ -19,6 +19,21 @@ rule all_metagenomics_host_depleted:
                     "{sample}.cleaned.{method}.krona.html"), sample=samples, method=['kraken', 'rna_bwa'])
     params: LSF='-N'
 
+rule all_kraken:
+    input:
+        expand(join(config["data_dir"], config["subdirs"]["metagenomics"],
+                    "{sample}.raw.kraken.report"), sample=samples),
+        expand(join(config["data_dir"], config["subdirs"]["metagenomics"],
+                    "{sample}.raw.kraken.krona.html"), sample=samples)
+    params: LSF='-N'
+
+rule all_kraken_host_depleted:
+    input:
+        expand(join(config["data_dir"], config["subdirs"]["metagenomics"],
+                    "{sample}.cleaned.kraken.report"), sample=samples),
+        expand(join(config["data_dir"], config["subdirs"]["metagenomics"],
+                    "{sample}.cleaned.kraken.krona.html"), sample=samples)
+    params: LSF='-N'
 
 method_props = {
     'diamond': {