Delete table.smk

workflow/rules/Multi/Catalogue/table.smk

-# if done: kraken to table: taxonomy per gene
-# if done: mapping to table: depth of coverage per gene in each sample - normalize by total reads (MG and MT); reads per sample?
-# if mapping done: summarize mapping: % samples with any coverage (MG and MT)s
-
-# rule cluster2tab:
-#    input:
-#        "Catalogue/catalogue_cluster.tsv"
-#    output:
-#        "Catalogue/catalogue_genesPerRep.tsv"
-#    threads: 1
-#    resources:
-#        runtime = "12:00:00",
-#        mem = MEMCORE
-#    params:
-#        sample = samples
-#    log: "logs/catalogue_cluster2tab.log"
-#    message: 'catalogue_cluster2tab: checking number of genes represented by each representative.'
-#    threads: 1
-#    script:
-#        SRCDIR + "/cluster2tab.py"
-
-rule gff2tab:
-    input:
-        "Catalogue/catalogue.gff"
-    output:
-        "Catalogue/catalogue_anno.tsv"
-    threads: 1
-    resources:
-        runtime = "12:00:00",
-        mem = MEMCORE
-    params:
-        dbs = config['hmm_DBs'].split()
-    log: "logs/catalogue_gff2tab.log"
-    message: 'gff2tab: extracting gff for catalogue info.'
-    threads: 1
-    script:
-        SRCDIR + "/gff2tab.py"
-
-rule catalogue_tab:
-    input:
-        getCatIn
-    output:
-        "Catalogue/catalogue.tsv"
-    resources:
-        runtime = "12:00:00",
-        mem = BIGMEMCORE
-    params:
-        types = TYPES
-    threads: 1
-    log: "logs/catalogue_tab.log"
-    conda: ENVDIR + "/IMP_multi.yaml"
-    message: "catalogue_tab: Merging results of catalogue."
-    script:
-        SRCDIR + "/multi_catalogue_merge.R"
-