correct paired argument parsing and length retrieval

rnabioco · Aug 28, 2024 · cf31eaa · cf31eaa
1 parent c5b2539
commit cf31eaa
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/rules/count.snake b/rules/count.snake
@@ -1,6 +1,6 @@
 """ Extract correction length target"""
 def _get_chem_length_R1(wildcards):
-    return CHEMISTRY[_get_config(wildcards.sample, "chemistry")]["filter_R1_length"]
+    return _get_config(wildcards.sample, "filter_R1_length")
 
 """ rules for scraps counting """
 

diff --git a/rules/cutadapt_star.snake b/rules/cutadapt_star.snake
@@ -30,6 +30,8 @@ def _get_chem_version(sample, alignment):
       extra_args = _get_config(sample, alignment+"_extra_args")
     except KeyError:
       extra_args = ""
+    if alignment == "STAR_paired":
+      alignment = "STAR_R1"
     return [whitelist, _get_config(sample, alignment), extra_args]
 
 """ Extract per-capture chemistry from gex libs (R2)"""
@@ -42,7 +44,7 @@ def _get_chem_version_R1(wildcards):
 
 """ Extract per-capture extra arguments for gex paired alignments """
 def _get_chem_version_paired(wildcards):
-    return _get_chem_version(wildcards.sample, "STAR_R1") + [_get_config(wildcards.sample, "STAR_paired")]
+    return _get_chem_version(wildcards.sample, "STAR_paired") + [_get_config(wildcards.sample, "STAR_paired")]
 
 """ This rule trims R1-only libraries """
 rule cutadapt_R1: