changed init: fixed a bug and rm unsed file (issue #56)

workflow/rules/init.smk

@@ -48,7 +48,7 @@ else:
         INPUT_LINKS[fast5] = os.path.join(RESULTS_DIR, "input/metag/ont/{fast5}".format(fast5=os.path.basename(fast5)))
 for mtype in META_TYPES:
     INPUT_LINKS[config["data"][mtype]["sr"]["r1"]] = os.path.join(RESULTS_DIR, "input/{mtype}/sr/R1.fq.gz".format(mtype=mtype))
-    INPUT_LINKS[config["data"][mtype]["sr"]["r1"]] = os.path.join(RESULTS_DIR, "input/{mtype}/sr/R2.fq.gz".format(mtype=mtype))
+    INPUT_LINKS[config["data"][mtype]["sr"]["r2"]] = os.path.join(RESULTS_DIR, "input/{mtype}/sr/R2.fq.gz".format(mtype=mtype))
 
 rule link_input_files:
     input:

workflow/rules/prepare_input.smk

-# Prepare input data
-
-localrules: link_input_files
-
-rule link_input_files:
-    input:
-        INPUT_G_FAST5 + INPUT_G_SR + INPUT_T_SR
-    output:
-        INPUT_LINKS
-    message:
-        "Link input files"
-    run:
-        assert len(input) == len(output), "Input and output lists have different length"
-        for ifname, ofname in zip(input, output):
-            # print("{} ==> {}".format(ifname, ofname))
-            os.symlink(os.path.abspath(ifname), ofname, target_is_directory=False)