fixed symlink errors

SNAKEFILE

@@ -1693,6 +1693,8 @@ rule hybrid_merge_bam_files_for_metaspades:
 ###########
 # Binning #
 ###########
+# Need to edit the first rule and find a way to incorporate wildcards to make it less UGLY. Also, for some reason, symlinks did not seem to work, so switching to hardlinks
+
 rule prepare_assembly_files:
     input:
          ass1=os.path.join(RESULTS_DIR, "assembly/flye/lr/merged/barcode07/assembly.fasta"),
@@ -1704,21 +1706,46 @@ rule prepare_assembly_files:
          fa1=os.path.join(RESULTS_DIR, "assembly/flye.fa"), 
          fa2=os.path.join(RESULTS_DIR, "assembly/megahit.fa"), 
          fa3=os.path.join(RESULTS_DIR, "assembly/metaspades_hybrid.fa"),
-         fa4=expand(os.path.join(RESULTS_DIR, "assembly/{mapper}_{reads}_{hybrid_assembler}.fa"), mapper=["bwa", "mmi"], reads=["sr", "lr", "merged"], hybrid_assembler=HYBRID_ASSEMBLER),
+#         fa4=expand(os.path.join(RESULTS_DIR, "assembly/{mapper}_{reads}_{hybrid_assembler}.fa"), mapper=["bwa", "mmi"], reads=["sr", "lr", "merged"], hybrid_assembler=HYBRID_ASSEMBLER),
+         fa4=os.path.join(RESULTS_DIR, "assembly/bwa_sr_metaspades_hybrid.fa"),
+         fa5=os.path.join(RESULTS_DIR, "assembly/bwa_lr_metaspades_hybrid.fa"),
+         fa6=os.path.join(RESULTS_DIR, "assembly/bwa_merged_metaspades_hybrid.fa"),
+         fa7=os.path.join(RESULTS_DIR, "assembly/mmi_sr_metaspades_hybrid.fa"),
+         fa8=os.path.join(RESULTS_DIR, "assembly/mmi_lr_metaspades_hybrid.fa"),
+         fa9=os.path.join(RESULTS_DIR, "assembly/mmi_merged_metaspades_hybrid.fa"),
          bout1=os.path.join(RESULTS_DIR, "mapping/megahit/megahit.bam"),
          bout2=os.path.join(RESULTS_DIR, "mapping/flye/flye.bam")
     shell:
+#         """
+#         (date &&\
+#         ln -s {input.ass1} {output.fa1} &&\
+#         ln -s {input.ass2} {output.fa2} &&\
+#         ln -s {input.ass3} {output.fa3} &&\
+#         ln -s {input.ass3} {output.fa4} &&\
+#         ln -s {input.ass3} {output.fa5} &&\
+#         ln -s {input.ass3} {output.fa6} &&\
+#         ln -s {input.ass3} {output.fa7} &&\
+#         ln -s {input.ass3} {output.fa8} &&\
+#         ln -s {input.ass3} {output.fa9} &&\
+#         ln -s {input.bam1} {output.bout1} &&\
+#         ln -s {input.bam2} {output.bout2} &&\
+#         date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
+#         """
          """
          (date &&\
-         ln -s {input.ass1} {output.fa1} &&\
-         ln -s {input.ass2} {output.fa2} &&\
-         ln -s {input.ass3} {output.fa3} &&\
-         ln -s {input.ass3} {output.fa4} &&\
-         ln -s {input.bam1} {output.bout1} &&\
-         ln -s {input.bam2} {output.bout2} &&\
+         ln {input.ass1} {output.fa1}
+         ln {input.ass2} {output.fa2}
+         ln {input.ass3} {output.fa3}
+         ln {input.ass3} {output.fa4}
+         ln {input.ass3} {output.fa5}
+         ln {input.ass3} {output.fa6}
+         ln {input.ass3} {output.fa7}
+         ln {input.ass3} {output.fa8}
+         ln {input.ass3} {output.fa9}
+         ln {input.bam1} {output.bout1}
+         ln {input.bam2} {output.bout2} 
          date) 2> >(tee {log}.stderr) > >(tee {log}.stdout)
          """
-
    
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