renamed mash rules

workflow/rules/analysis.smk

@@ -170,7 +170,7 @@ rule circ_contigs_filter:
 # Mash
 
 # Assemblies
-rule mash_sketch:
+rule analysis_mash_sketch:
     input:
         os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
     output:
@@ -184,7 +184,7 @@ rule mash_sketch:
     shell:
         "(date && ofile={output} && mash sketch -k 31 -s 10000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
 
-rule mash_sketch_paste:
+rule analysis_mash_sketch_paste:
     input:
         lr=expand(os.path.join(RESULTS_DIR, "assembly/lr/{tool}/ASSEMBLY.msh"), tool=config["assemblers"]["lr"]),
         sr=expand(os.path.join(RESULTS_DIR, "assembly/sr/{tool}/ASSEMBLY.msh"), tool=config["assemblers"]["sr"]),
@@ -198,7 +198,7 @@ rule mash_sketch_paste:
     shell:
         "ofile={output} && mash paste ${{ofile%.*}} {input}"
     
-rule mash_dist:
+rule analysis_mash_dist:
     input:
         os.path.join(RESULTS_DIR, "analysis/mash/contigs.msh")
     output:
@@ -215,7 +215,7 @@ rule mash_dist:
         "date) &> {log}"
 
 # Contigs
-rule mash_sketch_contigs:
+rule analysis_mash_sketch_contigs:
     input:
         os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
     output:
@@ -229,7 +229,7 @@ rule mash_sketch_contigs:
     shell:
         "(date && ofile={output} && mash sketch -i -k 31 -s 1000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
 
-rule mash_screen_contigs:
+rule analysis_mash_screen_contigs:
     input:
         fasta=expand(os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.FILTERED.fasta"), rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]),
         msh=expand(os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.contigs.msh"), rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS])