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Cedric Midoux
deepomics16S
Commits
c16471f6
Commit
c16471f6
authored
Apr 10, 2019
by
Cedric Midoux
Browse files
no biom, tsv export
parent
5ade9a3c
Changes
3
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Inline
Side-by-side
dada2.smk
View file @
c16471f6
...
...
@@ -12,9 +12,9 @@ rule makeSequenceTable:
input:
expand("work/dada/{sample}.rds", sample=SAMPLES)
output:
table
= "work/dada/seqtab.rds",
rds
= "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta",
biom
= "work/dada/
dada2.biom
"
tsv
= "work/dada/
seqtab.tsv
"
threads:
config["THREADS"]
script:
...
...
global.smk
View file @
c16471f6
...
...
@@ -7,8 +7,8 @@ rule all:
input:
"report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES),
"work/dada/seqtab.
rds
",
"work/dada/seqtab.
fasta
"
"work/dada/seqtab.
fasta
",
"work/dada/seqtab.
tsv
"
include: "quality.smk"
include: "preprocess.smk"
...
...
makeSequenceTable.R
View file @
c16471f6
library
(
dada2
)
library
(
biomformat
)
dada_list
<-
lapply
(
snakemake
@
input
,
readRDS
)
names
(
dada_list
)
<-
lapply
(
snakemake
@
input
,
function
(
x
){
basename
(
tools
::
file_path_sans_ext
(
x
))})
...
...
@@ -7,9 +6,8 @@ names(dada_list) <- lapply(snakemake@input, function(x){basename(tools::file_pat
seqtab
<-
makeSequenceTable
(
dada_list
,
orderBy
=
"abundance"
)
seqtab.nochim
<-
removeBimeraDenovo
(
seqtab
,
method
=
"consensus"
,
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
saveRDS
(
seqtab.nochim
,
snakemake
@
output
$
table
)
saveRDS
(
seqtab.nochim
,
snakemake
@
output
$
rds
)
uniquesToFasta
(
seqtab.nochim
,
snakemake
@
output
$
fasta
)
biom
<-
make_biom
(
t
(
seqtab.nochim
))
write_biom
(
biom
,
snakemake
@
output
$
biom
)
write.table
(
t
(
seqtab.nochim
),
snakemake
@
output
$
tsv
,
sep
=
"\t"
,
quote
=
FALSE
)
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