Missing feature_type in some GRO-seq output.

PRO-seq/PRO-seq.snakefile

@@ -380,7 +380,7 @@ rule all:
         # TODO: Add metagene profiles similar to small RNA-seq
         expand(OPJ(
             "{trimmer}", "figures", aligner, "{lib}_by_{norm_type}_mean",
-            "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)),
+            "{orientation}_transcript_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)),
             trimmer=TRIMMERS, lib=LIBS, norm_type=NORM_TYPES, orientation=["all", "fwd", "rev"],
             biotype=METAGENE_BIOTYPES),
 
@@ -1146,7 +1146,7 @@ rule make_normalized_bigwig:
 
 
 def source_bigwigs_for_merge(wildcards):
-    return [OPJ("{trimmer}".format(trimmer=wildcards.trimmer), aligner, "mapped_C_elegans", "{lib}_{{rep}}_on_C_elegans_by_{norm_type}_{orientation}.bw".format(lib=wildcards.lib, norm_type=wildcards.norm_type, orientation=wildcards.orientation).format(rep=rep)) for rep in REPS if frozenset((wildcards.lib, rep)) not in forbidden]
+    return [OPJ("{trimmer}".format(trimmer=wildcards.trimmer), aligner, "mapped_C_elegans", "{lib}_{{rep}}_on_C_elegans_by_{norm_type}_{orientation}_{feature_type}.bw".format(lib=wildcards.lib, norm_type=wildcards.norm_type, orientation=wildcards.orientation, feature_type=wildcards.feature_type).format(rep=rep)) for rep in REPS if frozenset((wildcards.lib, rep)) not in forbidden]
     #return expand(OPJ(aligner, "mapped_C_elegans", "{lib}_{rep}_on_C_elegans_norm_{orientation}.bw"), lib=[wildcards.lib], rep=[rep for rep in REPS if frozenset((wildcards.lib, rep)) not in forbidden], orientation=[wildcards.orientation])
 
 
@@ -1156,9 +1156,9 @@ rule merge_bigwig_reps:
         source_bigwigs_for_merge,
         #expand(OPJ(aligner, "mapped_C_elegans", "{{lib}}_{rep}_on_C_elegans_norm_{{orientation}}.bw"), rep=[rep for rep in REPS if frozenset((wildcards.lib, rep)) not in forbidden]),
     output:
-        bw = OPJ("{trimmer}", aligner, "mapped_C_elegans", "{lib}_mean_on_C_elegans_by_{norm_type}_{orientation}.bw"),
+        bw = OPJ("{trimmer}", aligner, "mapped_C_elegans", "{lib}_mean_on_C_elegans_by_{norm_type}_{orientation}_{feature_type}.bw"),
     log:
-        warnings = OPJ(log_dir, "{trimmer}", "merge_bigwig_reps", "{lib}_mean_on_C_elegans_by_{norm_type}_{orientation}.warnings"),
+        warnings = OPJ(log_dir, "{trimmer}", "merge_bigwig_reps", "{lib}_mean_on_C_elegans_by_{norm_type}_{orientation}_{feature_type}.warnings"),
     threads: 2  # to limit memory usage, actually
     run:
         with warn_context(log.warnings) as warn:
@@ -1703,7 +1703,7 @@ rule plot_meta_profile_mean:
         bigwig = rules.merge_bigwig_reps.output.bw,
         bed = rules.select_genes_for_meta_profile.output.out_bed,
     output:
-        OPJ("{trimmer}", "figures", aligner, "{lib}_by_{norm_type}_mean", "{orientation}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)),
+        OPJ("{trimmer}", "figures", aligner, "{lib}_by_{norm_type}_mean", "{orientation}_{feature_type}_on_merged_isolated_%d_{biotype}_min_%d_meta_profile.pdf" % (MIN_DIST, META_MIN_LEN)),
     params:
         meta_params = meta_params,
         # before = META_MARGIN,