updated targets in mapping step (issue #66)

workflow/steps/mapping.smk

@@ -11,7 +11,7 @@ rule MAPPING:
         ),
         metat=expand(
             os.path.join(RESULTS_DIR, "mapping/metat/{rtype_tool}.bam"),
-            rtype_tool=["{r}/{t}/ASSEMBLY_sr".format(r=r, t=t) for r, t in READ_ASSEMBLERS]
+            rtype_tool=["{r}/{t}/ASSEMBLY.FILTERED.sr".format(r=r, t=t) for r, t in READ_ASSEMBLERS]
         ) if "metat" in META_TYPES else []
     output:
         touch("status/mapping.done")
@@ -24,7 +24,7 @@ rule COVERAGE:
         ),
         metat=expand(
             os.path.join(RESULTS_DIR, "mapping/metat/{rtype_tool}.cov.ave.txt"),
-            rtype_tool=["{r}/{t}/ASSEMBLY_sr".format(r=r, t=t) for r, t in READ_ASSEMBLERS]
+            rtype_tool=["{r}/{t}/ASSEMBLY.FILTERED.sr".format(r=r, t=t) for r, t in READ_ASSEMBLERS]
         ) if "metat" in META_TYPES else []
     output:
         touch("status/coverage.done")
@@ -33,12 +33,12 @@ rule MAPPABILITY:
     input:
         metag=expand(
             os.path.join(RESULTS_DIR, "mapping/metag/{rtype_tool}.{ext}"),
-            rtype_tool=["{r}/{t}/ASSEMBLY_{r}".format(r=r, t=t) for r, t in READ_ASSEMBLERS],
+            rtype_tool=["{r}/{t}/ASSEMBLY.FILTERED.{r}".format(r=r, t=t) for r, t in READ_ASSEMBLERS],
             ext=["flagstat.txt", "idxstats.txt", "unique.txt"]
         ),
         metat=expand(
             os.path.join(RESULTS_DIR, "mapping/metat/{rtype_tool}.{ext}"),
-            rtype_tool=["{r}/{t}/ASSEMBLY_sr".format(r=r, t=t) for r, t in READ_ASSEMBLERS],
+            rtype_tool=["{r}/{t}/ASSEMBLY.FILTERED.sr".format(r=r, t=t) for r, t in READ_ASSEMBLERS],
             ext=["flagstat.txt", "idxstats.txt", "unique.txt"]
         ) if "metat" in META_TYPES else []
     output: