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Commit eb7c1faf authored by Midoux Cedric's avatar Midoux Cedric

metabat

parent acb0e2b9
......@@ -54,7 +54,7 @@ rule cd_hit:
"-i {input} "
"-o {output.ffn} "
"-c 0.95 "
"-G 1 "
"-g 1 "
"-aS 0.90 "
"-d 0 "
"-M 0 "
......@@ -106,3 +106,56 @@ rule faa_catalogue:
"{input.faa} "
" ; "
"conda deactivate"
checkpoint metabat:
input:
unpack(contigs_input)
output:
clusters = directory("work/metabat/{sample}")
params:
#output = "{output}/{sample}",
output = "work/metabat/{sample}/{sample}",
clustrsize = 200000
threads:
8
shell:
"conda activate metabat2-2.12.1 "
" ; "
"metabat2 "
"--inFile {input} "
"--outFile {params.output} "
"--minContig 5000 "
"--minClsSize {params.clustrsize} "
"--numThreads {threads} "
"--onlyLabel "
"--unbinned "
"--verbose "
" ; "
"conda deactivate "
rule metabat_kaiju:
input:
clustr = "work/metabat/{sample}/{sample}.{num}",
kaiju = "report/contigs_{sample}-taxNames.tsv"
output:
"work/metabat/{sample}/{sample}.{num}_kaiju.tsv"
shell:
"grep "
"--no-messages "
"--word-regexp "
"--file {input.clustr} "
"{input.kaiju} "
" > "
"{output} "
def aggregate_metabat(wildcards):
checkpoint_output = checkpoints.metabat.get(**wildcards).output.clusters
return expand("work/metabat/{sample}/{sample}.{i}_kaiju.tsv", sample=wildcards.sample, i=glob_wildcards(os.path.join(checkpoint_output, "{sample}.{i}")).i)
rule resume_metabat:
input:
aggregate_metabat
output:
done = temp("work/metabat/{sample}.done")
shell:
"touch {output.done} "
......@@ -30,5 +30,10 @@
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem=4G"
},
"metabat_kaiju" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l big_mem"
}
}
......@@ -16,6 +16,7 @@ rule all:
"report/diamond_swissprot_coassembly.tsv",
"report/contigs_coassembly-taxNames.tsv",
"report/genes_coassembly-taxNames.tsv",
"work/metabat/coassembly.done",
#catalogue
"report/quast_results/report.html",
expand("report/count-contigs-catalogue-{sample}.tsv", sample=config["SAMPLES"]),
......
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