updated step metaT

Snakefile

@@ -84,10 +84,10 @@ if 'mmseq' in STEPS:
         "mmseq_comparison_for_ont.done"
     ]
 
-# if 'metaT' in STEPS:
-#     include:
-#         "workflows/metat.smk"
-#     TARGETS += ["metaT_mapping_for_ONT.done"]
+if 'metaT' in STEPS:
+    include:
+        "workflow/steps/metat.smk"
+    TARGETS += ["metaT_mapping_for_ONT.done"]
 
 # if 'mapping' in STEPS:
 #     include:

workflow/steps/metat.smk

@@ -2,13 +2,13 @@
 
 # specify which rules to run
 include:
-    '../rules/METAT_RULES'
+    '../rules/metat.smk'
 
 # Rule all for mappinng metaT reads to all assemblies
 rule METAT:
     input:
         expand(os.path.join(RESULTS_DIR, "preprocessing/metaT/{metaT_sample}.fastp.{report_type}"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", report_type=["html", "json"]),
-#       expand(os.path.join(RESULTS_DIR, "mapping/metaT/lr/{metaT_sample}-x-{barcode}.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", barcode=BARCODES),
+        # expand(os.path.join(RESULTS_DIR, "mapping/metaT/lr/{metaT_sample}-x-{barcode}.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", barcode=BARCODES),
         expand(os.path.join(RESULTS_DIR, "mapping/metaT/sr/{metaT_sample}_reads-x-{sr_sample}-{assembler}_contigs.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", sr_sample="ONT3_MG_xx_Rashi_S11", assembler="megahit"),
         expand(os.path.join(RESULTS_DIR, "mapping/metaT/sr/{metaT_sample}_reads-x-lr_{barcode}_sr_{sr_sample}-{assembler}_contigs.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", sr_sample="ONT3_MG_xx_Rashi_S11", barcode=BARCODES, assembler="metaspades_hybrid"),
         expand(os.path.join(RESULTS_DIR, "mapping/metaT/lr/{metaT_sample}_reads-x-{barcode}-{assembler}_contigs.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", barcode=BARCODES, assembler=ASSEMBLERS),