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Cedric Midoux
deepomics16S
Commits
053aff9e
Commit
053aff9e
authored
Apr 11, 2019
by
Cedric Midoux
Browse files
DADA2 biom
parent
c16471f6
Changes
2
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dada2.smk
View file @
053aff9e
...
...
@@ -14,7 +14,8 @@ rule makeSequenceTable:
output:
rds = "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta",
tsv = "work/dada/seqtab.tsv"
tsv = "work/dada/seqtab.tsv",
biom = "work/dada/dada.biom"
threads:
config["THREADS"]
script:
...
...
makeSequenceTable.R
View file @
053aff9e
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
))})
...
...
@@ -11,3 +12,6 @@ saveRDS(seqtab.nochim, snakemake@output$rds)
uniquesToFasta
(
seqtab.nochim
,
snakemake
@
output
$
fasta
)
write.table
(
t
(
seqtab.nochim
),
snakemake
@
output
$
tsv
,
sep
=
"\t"
,
quote
=
FALSE
)
biom
<-
make_biom
(
t
(
seqtab.nochim
))
write_biom
(
biom
,
snakemake
@
output
$
biom
)
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