fix prefix issues

BIMSBbioinfo · Sep 12, 2024 · 423e21a · 423e21a
1 parent cd5c047
commit 423e21a
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/rules/export_tabix_bigwig.py b/rules/export_tabix_bigwig.py
@@ -32,8 +32,8 @@ def destrand(context):
     output:
         bw = os.path.join(DIR_bigwig, "{prefix}.{context}_{tool}.bw")
     wildcard_constraints:
-        context=".+(?<!destranded)",
-        tool="(?<!destranded)_.*"
+        context="CpG|CHG|CHH",
+        tool="methylDackel|methylKit"
     params:
         assembly = ASSEMBLY,
         destrand = lambda wc: destrand(wc.context)

diff --git a/rules/preprocessing_methyldackel.py b/rules/preprocessing_methyldackel.py
@@ -192,13 +192,11 @@ def keepDups(protocol):
     output:
         DIR_methcall + "methylDackel/" + "tabix_{context}/{prefix}_{context}.txt.bgz",
         DIR_methcall + "methylDackel/" + "tabix_{context}/{prefix}_{context}.txt.bgz.tbi"
-    wildcard_constraints:
-        sample="sorted.+(?<!deduped)"
     params:
         sampleid = "{prefix}_{context}",
         assembly = ASSEMBLY,
         treatment = lambda wc: samplesheet(
-            wc.prefix.replace(".deduped", ""), 'Treatment'),
+            removeMapperSuffix(wc.prefix), 'Treatment'),
         context = "{context}",
         dbdir = DIR_methcall + "methylDackel/" + "/tabix_{context}/",
         mincov = int(config['general']['methylation-calling']

diff --git a/scripts/func_defs.py b/scripts/func_defs.py
@@ -338,7 +338,7 @@ def bigwig_exporting_bismark(files, sampleID, protocol):
     if USEBWAMETH:
         INFIX += [ ".bwameth.sorted"]
     DESTRAND = "_destranded" if destrand("cpg") else ""
-    FILES = [ PATH+sampleID+infix + ".CpG" + DESTRAND + "_methylDackel" + ".bw" for infix in INFIX]
+    FILES = [ PATH+sampleID+infix+dedupe_tag(protocol) + ".CpG" + DESTRAND + "_methylDackel" + ".bw" for infix in INFIX]
     return FILES
 
 # FIXME: contexts should be generate output based on settings file