mash: rm contig-screen analysis, fixed a bug (not all assemblies included in assembly sketch)

workflow/rules/analysis.smk

@@ -188,7 +188,7 @@ rule analysis_mash_sketch_sr:
     conda:
         os.path.join(ENV_DIR, "mash.yaml")
     shell:
-        "(date && ofile={output} && mash sketch -r -m 2 -k 31 -s 10000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
+        "(date && ofile={output} && mash sketch -r -m 2 -k 31 -s 100000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
 
 rule analysis_mash_sketch_lr:
     input:
@@ -201,7 +201,7 @@ rule analysis_mash_sketch_lr:
     conda:
         os.path.join(ENV_DIR, "mash.yaml")
     shell:
-        "(date && ofile={output} && mash sketch -r -m 2 -k 31 -s 10000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
+        "(date && ofile={output} && mash sketch -r -m 2 -k 31 -s 100000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
 
 rule analysis_mash_paste_reads:
     input:
@@ -241,13 +241,14 @@ rule analysis_mash_sketch_asm:
     conda:
         os.path.join(ENV_DIR, "mash.yaml")
     shell:
-        "(date && ofile={output} && mash sketch -k 31 -s 10000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
+        "(date && ofile={output} && mash sketch -k 31 -s 100000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
 
 rule analysis_mash_paste_asm:
     input:
-        lr=expand(os.path.join(RESULTS_DIR, "assembly/lr/{tool}/ASSEMBLY.FILTERED.msh"), tool=config["assemblers"]["lr"]),
-        sr=expand(os.path.join(RESULTS_DIR, "assembly/sr/{tool}/ASSEMBLY.FILTERED.msh"), tool=config["assemblers"]["sr"]),
-        hy=expand(os.path.join(RESULTS_DIR, "assembly/hy/{tool}/ASSEMBLY.FILTERED.msh"), tool=config["assemblers"]["hy"])
+        expand(
+            os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.FILTERED.msh"),
+            rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS],
+        )
     output:
         os.path.join(RESULTS_DIR, "analysis/mash/contigs.msh")
     threads: 1

workflow/steps/analysis.smk

@@ -30,9 +30,9 @@ rule ANALYSIS:
             os.path.join(RESULTS_DIR, "analysis/mash/{dtype}.dist"),
             dtype=["contigs", "reads"]
         ) if "mash_dist" in config["steps_analysis"] else [],
-        expand(
-            os.path.join(RESULTS_DIR, "analysis/mash/screen.{rtype_tool}.tsv"),
-            rtype_tool=["%s.%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]
-        ) if "mash_screen" in config["steps_analysis"] else [],
+        # expand(
+        #     os.path.join(RESULTS_DIR, "analysis/mash/screen.{rtype_tool}.tsv"),
+        #     rtype_tool=["%s.%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]
+        # ) if "mash_screen" in config["steps_analysis"] else [],
     output:
         touch("status/analysis.done")