preseq new version, use shell command

workflow/rules/post-analysis.smk

@@ -7,8 +7,10 @@ rule preseq_lc_extrap:
          "-v {} -seed 1".format( "" if config["single_end"] else "-pe" )
     log:
         "logs/preseq/{sample}.log"
-    wrapper:
-        "0.64.0/bio/preseq/lc_extrap"
+    shell:
+        """
+        preseq lc_extrap {params} -output {output} {input}  2> {log}
+        """
 
 rule collect_multiple_metrics:
     input:
@@ -199,7 +201,7 @@ rule phantompeakqualtools:
     conda:
         "../envs/phantompeakqualtools.yaml"
     shell:
-        "( Rscript -e \"library(caTools); source('../workflow/scripts/run_spp.R')\" "
+        "( Rscript -e \"library(caTools); source('workflow/scripts/run_spp.R')\" "
         "  -c={input} -savp={output.plot} -savd={output.r_data} "
         "  -out={output.res_phantom} -p={threads} 2>&1 ) >{log}"