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Cedric Midoux
deepomics16S
Commits
4b986440
Commit
4b986440
authored
Apr 05, 2019
by
Cedric Midoux
Browse files
fasta export
parent
c9084505
Changes
3
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dada2.smk
View file @
4b986440
...
...
@@ -12,7 +12,8 @@ rule makeSequenceTable:
input:
expand("work/dada/{sample}.rds", sample=SAMPLES)
output:
"work/dada/seqtab.rds"
table = "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta"
threads:
config["THREADS"]
script:
...
...
global.smk
View file @
4b986440
...
...
@@ -7,7 +7,8 @@ rule all:
input:
"report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.rds"
"work/dada/seqtab.rds",
"work/dada/seqtab.fasta"
include: "quality.smk"
include: "preprocess.smk"
...
...
makeSequenceTable.R
View file @
4b986440
...
...
@@ -2,4 +2,5 @@ library(dada2)
seqtab
<-
makeSequenceTable
(
lapply
(
snakemake
@
input
,
readRDS
),
orderBy
=
"abundance"
)
seqtab.nochim
<-
removeBimeraDenovo
(
seqtab
,
method
=
"consensus"
,
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
saveRDS
(
seqtab.nochim
,
snakemake
@
output
[[
1
]])
saveRDS
(
seqtab.nochim
,
snakemake
@
output
$
table
)
uniquesToFasta
(
seqtab.nochim
,
snakemake
@
output
$
fasta
)
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