reprocessing: rm realpath when linking

workflow/rules/preprocessing.smk

@@ -179,7 +179,7 @@ rule link_preproc_fastq_lr:
     output:
         os.path.join(RESULTS_DIR, "preproc/metag/lr/lr.proc.fastq.gz")
     shell:
-        "ln -sf $(realpath {input}) {output}"
+        "cd $(dirname ${output}) && ln -sf $(basename {input}) $(basename {output})"
 
 rule link_preproc_fastq_sr:
     input:
@@ -191,4 +191,6 @@ rule link_preproc_fastq_sr:
     wildcard_constraints:
         mtype="|".join(META_TYPES)
     shell:
-        "ln -sf $(realpath {input.r1}) {output.r1} && ln -sf $(realpath {input.r2}) {output.r2}"
\ No newline at end of file
+        "cd $(dirname ${output.r1}) && "
+        "ln -sf $(basename {input.r1}) $(basename {output.r1}) && "
+        "ln -sf $(basename {input.r2}) $(basename {output.r2})"
\ No newline at end of file