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centrifuge.smk
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centrifuge.smk
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rule download_centrifuge_taxonomy:
output:
name_table = "data/centrifuge_db/taxonomy/names.dmp",
tax_tree = "data/centrifuge_db/taxonomy/nodes.dmp",
threads: 1
resources:
mem_mb = 200
singularity:
config["container"]
log:
"logs/download_centrifuge_taxonomy.log"
shell:
"""
centrifuge-download -o data/centrifuge_db/taxonomy taxonomy 2> {log}
"""
rule download_centrifuge_library:
output:
mapping = "data/centrifuge_db/seqid2taxid.map",
library = directory("data/centrifuge_db/library")
threads: 1
resources:
mem_mb = 200
params:
domain = "archaea,bacteria"
singularity:
config["container"]
log:
"logs/download_centrifuge_library.log"
shell:
"""
centrifuge-download -o {output.library} -m -d {params.domain} refseq > {output.mapping} 2> {log}
"""
rule combine_centrifuge_library_sequences:
input:
rules.download_centrifuge_library.output.library
output:
temp("data/centrifuge_db/combined.fna")
threads: 1
resources:
mem_mb = 200
log:
"logs/combine_centrifuge_library_sequences.log"
shell:
"""
cat {input}/*/*.fna > {output} 2> {log}
"""
rule build_centrifuge_db:
input:
sequences = "data/centrifuge_db/combined.fna",
conversion_table = rules.download_centrifuge_library.output.mapping,
tax_tree = rules.download_centrifuge_taxonomy.output.tax_tree,
name_table = rules.download_centrifuge_taxonomy.output.name_table
output:
expand("data/centrifuge_db/archaea_bacteria.{db_idx}.cf", db_idx=range(1, 4))
threads:
config["build_centrifuge_db"]["threads"]
resources:
mem_mb = lambda wildcards, attempt: attempt * config["build_centrifuge_db"]["memory"]
params:
prefix = "data/centrifuge_db/archaea_bacteria"
singularity:
config["container"]
log:
"logs/build_centrifuge_db.log"
shell:
"""
centrifuge-build -p {threads} --conversion-table {input.conversion_table} \
--taxonomy-tree {input.tax_tree} --name-table {input.name_table} \
{input.sequences} {params.prefix} &> {log}
"""
rule centrifuge:
input:
rules.build_centrifuge_db.output,
fastq = "data/{run}/filtlong/{sample}.filtered.fastq.gz"
output:
report = "data/{run}/centrifuge/centrifuge_report_{run}_{sample}.tsv",
classification = "data/{run}/centrifuge/centrifuge_classification_{run}_{sample}.tab"
threads:
config["centrifuge"]["threads"]
resources:
mem_mb = lambda wildcards, attempt: attempt * config["centrifuge"]["memory"]
params:
index_prefix = "data/centrifuge_db/archaea_bacteria"
singularity:
config["container"]
log:
"logs/centrifuge_{run}_{sample}.log"
shell:
"""
centrifuge -x {params.index_prefix} \
-U {input.fastq} \
--threads {threads} \
--report-file {output.report} \
-S {output.classification} \
--met-stderr 2> {log}
"""
rule centrifuge_krakenstyle_report:
input:
"data/{run}/centrifuge/centrifuge_classification_{run}_{sample}.tab"
output:
"data/{run}/centrifuge/centrifuge_classification_{run}_{sample}.kreport"
threads: 1
resources:
mem_mb = 500
params:
index_prefix = "data/centrifuge_db/archaea_bacteria"
log:
"logs/centrifuge_kreport_{run}_{sample}.log"
singularity:
config["container"]
shell:
"""
centrifuge-kreport -x {params.index_prefix} {input} > {output} 2> {log}
"""
rule download_centrifuge_16s_resources:
output:
ref_seqs = "data/centrifuge_16s_db/data/SILVA_132_SSURef_Nr99_tax_silva.rna.fasta",
taxmap = "data/centrifuge_16s_db/data/taxmap_embl_ssu_ref_nr99_132.txt"
threads: 1
resources:
mem_mb = 500
params:
seq_url = "https://www.arb-silva.de/fileadmin/silva_databases/release_132/Exports/SILVA_132_SSURef_Nr99_tax_silva.fasta.gz",
taxmap_url = "https://www.arb-silva.de/fileadmin/silva_databases/release_132/Exports/taxonomy/taxmap_embl_ssu_ref_nr99_132.txt.gz",
log:
"logs/download_centrifuge_16s_resources.log"
shell:
"""
wget {params.seq_url} -O - | gzip -d -c - > {output.ref_seqs} 2> {log}
wget {params.taxmap_url} -O - | gzip -d -c - > {output.taxmap} 2>> {log}
"""
rule convert_silva_db_to_dna:
input:
"data/centrifuge_16s_db/data/SILVA_132_SSURef_Nr99_tax_silva.rna.fasta"
output:
"data/centrifuge_16s_db/data/SILVA_132_SSURef_Nr99_tax_silva.fasta"
threads: 1
resources:
mem_mb = 500
log:
"logs/convert_silva_db_to_dna.log"
wrapper:
"0.35.2-28-g9f45aaa/bio/pyfastaq/replace_bases"
rule make_centrifuge_16s_conversion_table:
input:
taxmap = rules.download_centrifuge_16s_resources.output.taxmap,
output:
conversion_table = "data/centrifuge_16s_db/seqid2taxid.map",
threads: 1
resources:
mem_mb = 300
log:
"logs/make_centrifuge_16s_conversion_table.log"
shell:
"""
awk '{{print $1\".\"$2\".\"$3\"\t\"$(NF)}}' {input.taxmap} > {output.conversion_table} 2> {log}
"""
rule build_centrifuge_16s_db:
input:
name_table = rules.download_centrifuge_taxonomy.output.name_table,
tax_tree = rules.download_centrifuge_taxonomy.output.tax_tree,
conversion_table = rules.make_centrifuge_16s_conversion_table.output.conversion_table,
ref_seqs = "data/centrifuge_16s_db/data/SILVA_132_SSURef_Nr99_tax_silva.fasta"
output:
expand("data/centrifuge_16s_db/silva_16s.{db_idx}.cf", db_idx=range(1, 5))
threads:
config["build_centrifuge_16s_db"]["threads"]
resources:
mem_mb = lambda wildcards, attempt: attempt * config["build_centrifuge_16s_db"]["memory"]
params:
prefix = "data/centrifuge_16s_db/silva_16s"
log:
"logs/build_centrifuge_16s_db.log"
singularity:
config["container"]
shell:
"""
centrifuge-build \
--threads {threads} \
--conversion-table {input.conversion_table} \
--taxonomy-tree {input.tax_tree} \
--name-table {input.name_table} \
{input.ref_seqs} \
{params.prefix} 2> {log}
"""
rule centrifuge_16s_classify:
input:
rules.build_centrifuge_16s_db.output,
fastq = "data/{run}/filtlong/{sample}.filtered.fastq.gz"
output:
report = "data/{run}/centrifuge/centrifuge_16s_report_{run}_{sample}.tsv",
classification = "data/{run}/centrifuge/centrifuge_16s_classification_{run}_{sample}.tab"
threads:
config["centrifuge_16s"]["threads"]
resources:
mem_mb = lambda wildcards, attempt: attempt * config["centrifuge_16s"]["memory"]
params:
index_prefix = "data/centrifuge_16s_db/silva_16s"
singularity:
config["container"]
log:
"logs/centrifuge_16s_classify_{run}_{sample}.log"
shell:
"""
centrifuge -x {params.index_prefix} \
-U {input.fastq} \
--threads {threads} \
--report-file {output.report} \
-S {output.classification} \
--met-stderr 2> {log}
"""
rule centrifuge_16s_krakenstyle_report:
input:
"data/{run}/centrifuge/centrifuge_16s_classification_{run}_{sample}.tab"
output:
"data/{run}/centrifuge/centrifuge_16s_classification_{run}_{sample}.kreport"
threads: 1
resources:
mem_mb = 500
params:
index_prefix = "data/centrifuge_16s_db/silva_16s"
log:
"logs/centrifuge_16s_kreport_{run}_{sample}.log"
singularity:
config["container"]
shell:
"""
centrifuge-kreport -x {params.index_prefix} {input} > {output} 2> {log}
"""