Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Cedric Midoux
deepomics16S
Commits
da4fa296
Commit
da4fa296
authored
Apr 04, 2019
by
Cedric Midoux
Browse files
DADA2
parent
9dfbb487
Changes
3
Hide whitespace changes
Inline
Side-by-side
dada2.R
0 → 100644
View file @
da4fa296
library
(
dada2
)
derep
<-
derepFastq
(
snakemake
@
input
[[
1
]],
verbose
=
TRUE
)
err
<-
learnErrors
(
snakemake
@
input
[[
1
]],
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
dada
<-
dada
(
derep
,
err
=
err
,
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
saveRDS
(
dada
,
snakemake
@
output
[[
1
]])
dada2.smk
0 → 100644
View file @
da4fa296
rule dada2:
input:
"work/filter/{sample}.fastq.gz"
output:
"work/dada/{sample}.rds"
threads:
config["THREADS"]
script:
"dada2.R"
global.smk
View file @
da4fa296
...
...
@@ -5,7 +5,9 @@ SAMPLES=config["SAMPLES"]
rule all:
input:
"report/multiqc_report.html"
"report/multiqc_report.html",
expand("work/dada/{sample}.rds", sample=SAMPLES)
include: "quality.smk"
include: "preprocess.smk"
include: "dada2.smk"
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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