Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
Open sidebar
Cedric Midoux
deepomics16S
Commits
79ec309d
Commit
79ec309d
authored
Apr 10, 2019
by
Cedric Midoux
Browse files
biom export
parent
4b986440
Changes
2
Hide whitespace changes
Inline
Side-by-side
dada2.smk
View file @
79ec309d
...
...
@@ -13,7 +13,8 @@ rule makeSequenceTable:
expand("work/dada/{sample}.rds", sample=SAMPLES)
output:
table = "work/dada/seqtab.rds",
fasta = "work/dada/seqtab.fasta"
fasta = "work/dada/seqtab.fasta",
biom = "work/dada/dada2.biom"
threads:
config["THREADS"]
script:
...
...
makeSequenceTable.R
View file @
79ec309d
library
(
dada2
)
library
(
biomformat
)
seqtab
<-
makeSequenceTable
(
lapply
(
snakemake
@
input
,
readRDS
),
orderBy
=
"abundance"
)
dada_list
<-
lapply
(
snakemake
@
input
,
readRDS
)
names
(
dada_list
)
<-
lapply
(
snakemake
@
input
,
function
(
x
){
basename
(
tools
::
file_path_sans_ext
(
x
))})
seqtab
<-
makeSequenceTable
(
dada_list
,
orderBy
=
"abundance"
)
seqtab.nochim
<-
removeBimeraDenovo
(
seqtab
,
method
=
"consensus"
,
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
saveRDS
(
seqtab.nochim
,
snakemake
@
output
$
table
)
uniquesToFasta
(
seqtab.nochim
,
snakemake
@
output
$
fasta
)
biom
<-
make_biom
(
seqtab.nochim
)
write_biom
(
biom
,
snakemake
@
output
$
biom
)
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment