Delete kraken_genes.smk

workflow/rules/Multi/Catalogue/kraken_genes.smk

-from os.path import getsize
-KRAKSIZE = float(os.path.getsize(DBPATH + "/" + config['catalogue']['kraken']['db'] + "/hash.k2d" )) / 1000000000
-KRAKTHREADS = round( (KRAKSIZE / float(BIGMEMCORE[:-1])) + 0.5)
-
-rule kraken_cat:
-    input:
-        "Catalogue/catalogue.fasta" 
-    output:
-        "Catalogue/catalogue_kraken.output",
-        "Catalogue/catalogue_kraken.report" 
-    resources:
-        runtime = "8:00:00",
-        mem = BIGMEMCORE
-    threads: getThreads(KRAKTHREADS)
-    conda: ENVDIR + "/IMP_taxonomy.yaml"
-    log: "logs/analysis_kraken_cat"
-    message: "kraken_cat: Running kraken2 on genes from catalog against {config[catalogue][kraken][db]}."
-    shell:	
-        """
-        kraken2 -db {DBPATH}/{config[catalogue][kraken][db]} --threads {threads} --use-names --report-zero-counts \
-         --output {output[0]} --report {output[1]} {input} >> {log} 2>&1
-        """
-
-rule kraken_parse_cat:
-    input:
-        "Catalogue/catalogue_kraken.output",
-        "Catalogue/catalogue_kraken.report"
-    output:
-        "Catalogue/catalogue_kraken.parsed.tsv" 
-    threads: 1
-    resources:
-        runtime = "2:00:00",
-        mem = MEMCORE
-    conda: ENVDIR + "/IMP_taxonomy.yaml"
-    log: "logs/analysis_kraken_parse_cat.log"
-    message: "kraken_parse_cat: Parsing kraken2 output for genes."
-    shell:
-        """
-        {SRCDIR}/krakenContigEntropy_dynamic.py -c {input[0]} -e 0.1 -o {output} -r {input[1]} > {log} 2>&1
-        """
-
-