save unmapped reads

openvax · Sep 25, 2018 · 53cd042 · 53cd042
1 parent e8243b8
commit 53cd042
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/docker/VERSION b/docker/VERSION
@@ -1 +1 @@
-0.2.0
+0.3.0
diff --git a/pipeline/rna.rules b/pipeline/rna.rules
@@ -45,6 +45,7 @@ if _rna_exists():
       "--outSAMstrandField intronMotif "
       "--outSAMattributes NH HI NM MD "
       "--outSAMmapqUnique 60 "
+      "--outSAMunmapped Within "
       "--outFilterIntronMotifs RemoveNoncanonical "
       "--outSAMattrRGline ID:{wildcards.prefix} SM:'{params.rg_sm}' "
       "--outFileNamePrefix {params.output_dir}/{wildcards.prefix} "
@@ -77,6 +78,7 @@ if _rna_exists():
       "--outSAMstrandField intronMotif "
       "--outSAMattributes NH HI NM MD "
       "--outSAMmapqUnique 60 "
+      "--outSAMunmapped Within "
       "--outFilterIntronMotifs RemoveNoncanonical "
       "--outSAMattrRGline ID:{wildcards.prefix} SM:'{params.rg_sm}' "
       "--outFileNamePrefix {params.output_dir}/{wildcards.prefix} "