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Midoux Cedric authored4ee40425
rule FragGeneScan:
input:
unpack(contigs_input)
output:
faa = "work/FGS/{sample}_FGS.faa",
ffn = "work/FGS/{sample}_FGS.ffn",
gff = "work/FGS/{sample}_FGS.gff",
out = temp("work/FGS/{sample}_FGS.out")
threads:
config["THREADS"]
params:
output = "work/FGS/{sample}_FGS"
shell:
"run_FragGeneScan.pl "
"-genome={input} "
"-out={params.output} "
"-complete=0 " #negative values with complete=1
"-train=complete "
"-thread={threads} "
" ; "
"sed --in-place 's/*/N/' {output.faa} "
rule prodigal:
input:
unpack(contigs_input)
output:
faa = "work/prodigal/{sample}_prodigal.faa",
ffn = "work/prodigal/{sample}_prodigal.ffn",
gff = "work/prodigal/{sample}_prodigal.gff"
shell:
"prodigal "
"-f gff "
"-i {input} "
"-a {output.faa} "
"-d {output.ffn} "
"-o {output.gff} "
"-g 11 "
"-po meta "
rule prokka:
input:
unpack(contigs_input)
output:
err = "work/prokka/{sample}_prokka.err",
faa = "work/prokka/{sample}_prokka.faa",
ffn = "work/prokka/{sample}_prokka.ffn",
fna = "work/prokka/{sample}_prokka.fna",
fsa = "work/prokka/{sample}_prokka.fsa",
gbk = "work/prokka/{sample}_prokka.gbk",
gff = "work/prokka/{sample}_prokka.gff",
log = "work/prokka/{sample}_prokka.log",
sqn = "work/prokka/{sample}_prokka.sqn",
tbl = "work/prokka/{sample}_prokka.tbl",
tsv = "work/prokka/{sample}_prokka.tsv",
txt = "work/prokka/{sample}_prokka.txt"
params:
output = lambda wildcards, output: os.path.dirname(str(output.gff)),
threads:
config["THREADS"]
shell:
"prokka "
"--output-dir {params.output} "
"--force "
"--prefix {wildcards.sample}_prokka "
"--gffver 3 "
"--metagenome "
"--cpus {threads} "
"--notrna "
"--norrna "
"{input} "
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rule diamond:
input:
faa = "work/FGS/{sample}_FGS.faa",
database = "/db/outils/diamond-0.9.24/nr_tax.dmnd"
output:
daa = "work/DIAMOND/{sample}.daa",
unaligned = "work/DIAMOND/{sample}_unaligned.faa"
threads:
config["THREADS"]
shell:
"diamond "
"blastp "
"--db {input.database} "
"--query {input.faa} "
"--sensitive "
"--max-target-seqs 1 "
"--threads {threads} "
"--out {output.daa} "
"--outfmt 100 "
"--salltitles "
"--sallseqid "
"--un {output.unaligned} "
"--verbose "
rule diamondView:
input:
daa = "work/DIAMOND/{sample}.daa"
output:
tsv = "report/diamond-NR_{sample}.tsv"
params:
keywords = "qseqid qlen sseqid sallseqid slen qstart qend sstart send qseq full_qseq sseq full_sseq evalue bitscore score length pident nident mismatch positive gapopen gaps ppos qframe btop stitle salltitles qcovhsp qtitle qqual" #staxids
shell:
"diamond "
"view "
"--daa {input.daa} "
"--outfmt 6 {params.keywords} "
"--out {output.tsv} "
"--header "
rule eggnog:
input:
faa = "work/FGS/{reads}_FGS.faa"
output:
hits = "work/eggnog/{reads}-{database}.emapper.hmm_hits",
orthologs = "work/eggnog/{reads}-{database}.emapper.seed_orthologs",
annotations = "work/eggnog/{reads}-{database}.emapper.annotations"
threads:
config["THREADS"]
params:
output = "work/eggnog/{reads}-{database}"
shell:
"emapper.py "
"--cpu {threads} "
"--database {wildcards.database} "
"--hmm_maxhits 1 "
"--output {params.output} "
"-i {input.faa} "
rule interproscan:
input:
faa = "work/FGS/{sample}_FGS.faa"
output:
tsv = "work/interproscan/{sample}_FGS.faa.tsv",
gff3 = "work/interproscan/{sample}_FGS.faa.gff3",
html = "work/interproscan/{sample}_FGS.faa.html.tar.gz"
params:
output = lambda wildcards, output: os.path.dirname(str(output.tsv)),
mem_tot = int(config["MEM"] * config["THREADS"] * 1e9)
threads:
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config["THREADS"]
shell:
"interproscan.sh "
"--cpu {threads} "
"--highmem {params.mem_tot} "
"--input {input.faa} "
"--seqtype p "
"--output-dir {params.output} "
"--formats tsv,gff3,html "
"--iprlookup "
"--goterms "
"--pathways "