analysis: rm unused code for mmseqs2

workflow/rules/analysis.smk

@@ -207,62 +207,3 @@ rule analysis_mash_screen_contigs:
         os.path.join(ENV_DIR, "mash.yaml")
     script:
         os.path.join(SRC_DIR, "mash_screen_contigs.py")
-
-##################################################
-# MMseqs2
-
-# rule analysis_mmseqs2_db:
-#     input:
-#         os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
-#     output:
-#         os.path.join(RESULTS_DIR, "analysis/mmseqs2/{rtype}/{tool}/ASSEMBLY_db")
-#     log:
-#         "logs/mmseqs2_db.{rtype}.{tool}.log"
-#     wildcard_constraints:
-#         rtype="|".join(READ_TYPES),
-#         tool="|".join(ASSEMBLERS)
-#     conda:
-#         os.path.join(ENV_DIR, "mmseqs2.yaml")
-#     message:
-#         "Create MMseqs2 DB from {input}"
-#     shell:
-#         "(date && mmseqs createdb {input} {output} && date) &> {log}"
-
-# rule analysis_mmseqs2_compare:
-#     input:
-#         db1=os.path.join(RESULTS_DIR, "analysis/mmseqs2/{rtype1}/{tool1}/ASSEMBLY_db"),
-#         db2=os.path.join(RESULTS_DIR, "analysis/mmseqs2/{rtype2}/{tool2}/ASSEMBLY_db")
-#     output:
-#         os.path.join(RESULTS_DIR, "analysis/mmseqs2/comparison/{rtype1}_{tool1}__{rtype2}_{tool2}")
-#     log:
-#         "logs/mmseqs2.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
-#     wildcard_constraints:
-#         rtype1="|".join(READ_TYPES),
-#         rtype2="|".join(READ_TYPES),
-#         tool1="|".join(ASSEMBLERS),
-#         tool2="|".join(ASSEMBLERS)
-#     threads:
-#         config["mmseqs2"]["threads"]
-#     conda:
-#         os.path.join(ENV_DIR, "cd-hit.yaml")
-#     message:
-#         "Create MMseqs2 compare: {input}"
-#     shell:
-#         # TODO: "mmseqs2_tmp" ??? (see old files)
-#         "(date && mmseqs rbh {input.db1} {input.db2} {output} --min-seq-id 0.9 --threads {threads} && date) &> {log}"
-
-# rule analysis_mmseqs2_m8_convert:
-#     input:
-#         db1=os.path.join(RESULTS_DIR, "analysis/mmseqs2/{rtype1}/{tool1}/ASSEMBLY_db"),
-#         db2=os.path.join(RESULTS_DIR, "analysis/mmseqs2/{rtype2}/{tool2}/ASSEMBLY_db"),
-#         rbh=os.path.join(RESULTS_DIR, "analysis/mmseqs2/comparison/{rtype1}_{tool1}__{rtype2}_{tool2}")
-#     output:
-#         os.path.join(RESULTS_DIR, "analysis/mmseqs2/comparison/{rtype1}_{tool1}__{rtype2}_{tool2}.m8")
-#     log:
-#         "logs/mmseqs2_convert.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
-#     conda:
-#         os.path.join(ENV_DIR, "cd-hit.yaml")
-#     message:
-#         "Create MMseqs2 compare: {input}"
-#     shell:
-#         "(date && mmseqs convertalis {input.db1} {input.db2} {input.rbh} {output} && date) &> {log}"