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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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Cedric Midoux
deepomics16S
Commits
c9084505
Commit
c9084505
authored
Apr 05, 2019
by
Cedric Midoux
Browse files
DADA2 makeSequenceTable
parent
da4fa296
Changes
3
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dada2.smk
View file @
c9084505
...
...
@@ -7,3 +7,13 @@ rule dada2:
config["THREADS"]
script:
"dada2.R"
rule makeSequenceTable:
input:
expand("work/dada/{sample}.rds", sample=SAMPLES)
output:
"work/dada/seqtab.rds"
threads:
config["THREADS"]
script:
"makeSequenceTable.R"
global.smk
View file @
c9084505
...
...
@@ -6,7 +6,8 @@ SAMPLES=config["SAMPLES"]
rule all:
input:
"report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES)
expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.rds"
include: "quality.smk"
include: "preprocess.smk"
...
...
makeSequenceTable.R
0 → 100644
View file @
c9084505
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
]])
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