rm workflow/steps/mapping.smk (incl in assembly)

workflow/steps/mapping.smk

-# Mapping
-
-include:
-    '../rules/mapping.smk'
-
-# NOTE: Using "shell: touch ..." to avoid the rule from being autodetected as `localrule`.
-#       This is needed so that an email can be sent upon event changes for this rule.
-
-rule MAPPING:
-    input:
-        lr=expand(os.path.join(RESULTS_DIR, "mapping/lr/{tool}/assembly_lr.bam"), tool=config["assemblers"]["lr"]),
-        sr=expand(os.path.join(RESULTS_DIR, "mapping/sr/{tool}/assembly_sr.bam"), tool=config["assemblers"]["sr"]),
-        hy=expand(
-            os.path.join(RESULTS_DIR, "mapping/{rtype1}/{tool}/assembly_{rtype2}.bam"),
-            rtype1=["hy"], rtype2=["sr", "lr", "hy"], tool=config["assemblers"]["hy"]
-        )
-    output:
-        "status/mapping.done"
-    shell:
-        "touch {output}"