Commit 0c08a3d1 authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

Delete affiliation.smk

parent da019b7b
rule addAffi:
input:
biom = "work/dada/dada.biom",
fasta = "work/dada/seqtab.fasta"
output:
biom = "work/FROGS/affiliation.biom",
html = "work/FROGS/affiliation.html",
log = "work/FROGS/affiliation.log"
threads:
config["THREADS"]
params:
database = config["DATABASE"]
shell:
"conda activate frogs-3.2.0 "
"&& "
"affiliation_OTU.py "
"--input-fasta {input.fasta} "
"--input-biom {input.biom} "
"--nb-cpu {threads} "
"--log-file {output.log} "
"--output-biom {output.biom} "
"--summary {output.html} "
"--reference {params.database} "
"&& "
"conda deactivate"
rule stats:
input:
biom = "work/FROGS/affiliation.biom"
output:
html_cluster = "work/FROGS/clusters_metrics.html",
html_affiliations = "work/FROGS/affiliations_metrics.html"
shell:
"conda activate frogs-3.2.0 "
"&& "
"clusters_stat.py "
"--input-biom {input.biom} "
"--output-file {output.html_cluster}"
"&& "
"affiliations_stat.py "
"--input-biom {input.biom} "
"--output-file {output.html_affiliations} "
"--taxonomic-ranks Domain Phylum Class Order Family Genus Species "
"--rarefaction-ranks Genus "
"--multiple-tag blast_affiliations "
"--tax-consensus-tag blast_taxonomy "
"--identity-tag perc_identity "
"--coverage-tag perc_query_coverage"
"&& "
"conda deactivate"
rule tree:
input:
fasta = "work/dada/seqtab.fasta",
biom = "work/FROGS/affiliation.biom"
output:
html = "work/FROGS/tree.html",
nwk = "work/FROGS/tree.nwk",
log = "work/FROGS/tree.log"
threads:
config["THREADS"]
shell:
"conda activate frogs-3.2.0 "
"&& "
"tree.py "
"--nb-cpus {threads} "
"--input-sequences {input.fasta} "
"--biom-file {input.biom} "
"--out-tree {output.nwk} "
"--html {output.html} "
"--log-file {output.log} "
"&& "
"conda deactivate"
rule stdBIOM:
input:
biom = "work/FROGS/affiliation.biom"
output:
biom = "work/FROGS/abundance.biom",
tsv = "work/FROGS/blast_informations.std.tsv"
shell:
"conda activate frogs-3.2.0 "
"&& "
"biom_to_stdBiom.py "
"--input-biom {input.biom} "
"--output-biom {output.biom} "
"--output-metadata {output.tsv}"
"&& "
"conda deactivate"
rule biom_to_tsv:
input:
biom = "work/FROGS/affiliation.biom",
fasta = "work/dada/seqtab.fasta"
output:
tsv = "work/FROGS/abundance.tsv",
multi = "work/FROGS/multihits.tsv"
shell:
"conda activate frogs-3.2.0 "
"&& "
"biom_to_tsv.py "
"--input-biom {input.biom} "
"--input-fasta {input.fasta} "
"--output-tsv {output.tsv} "
"--output-multi-affi {output.multi}"
"&& "
"conda deactivate"
localrules: copy
rule copy:
input:
"work/FROGS/{file}"
output:
"report/{file}"
shell:
"cp -uv {input} {output}"
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