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Cedric Midoux
deepomics16S
Commits
7e4d83e6
Commit
7e4d83e6
authored
Mar 24, 2021
by
Slaheddine Kastalli
Browse files
add paired ends and prefetch rule
parent
89a5a86f
Changes
7
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config.json
View file @
7e4d83e6
{
"THREADS"
:
8
,
"SAMPLES"
:
[
"4A"
,
"5A"
,
"6A"
,
"7A"
,
"8A"
,
"9A"
,
"10A"
,
"11A"
,
"12A"
],
"FIVE_PRIMER"
:
{
"4A"
:
"GTGYCAGCMGCCGCGGTA"
,
"5A"
:
"GTGYCAGCMGCCGCGGTA"
,
"6A"
:
"GTGYCAGCMGCCGCGGTA"
,
"7A"
:
"GTGYCAGCMGCCGCGGTA"
,
"8A"
:
"GTGYCAGCMGCCGCGGTA"
,
"9A"
:
"GTGYCAGCMGCCGCGGTA"
,
"10A"
:
"GTGYCAGCMGCCGCGGTA"
,
"11A"
:
"GTGYCAGCMGCCGCGGTA"
,
"12A"
:
"GTGYCAGCMGCCGCGGTA"
},
"THREE_PRIMER"
:
{
"4A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"5A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"6A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"7A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"8A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"9A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"10A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"11A"
:
"ACTYAAAKGAATTGRCGGGG"
,
"12A"
:
"ACTYAAAKGAATTGRCGGGG"
},
"THREADS"
:
1
,
"srr"
:
[
"SRR1187735"
],
"SAMPLES"
:
[
"SRR1187735"
],
"FIVE_PRIMER"
:
{
"SRR1187735"
:
"GTGYCAGCMGCCGCGGTA"
},
"THREE_PRIMER"
:
{
"SRR1187735"
:
"ACTYAAAKGAATTGRCGGGG"
},
"DATABASE"
:
"/db/frogs_databanks/assignation/16S/silva_132_16S_pintail100/silva_132_16S_pintail100.fasta"
}
dada2.R
View file @
7e4d83e6
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
)
derepF
<-
derepFastq
(
snakemake
@
input
[[
1
]],
verbose
=
TRUE
)
derepR
<-
derepFastq
(
snakemake
@
input
[[
2
]],
verbose
=
TRUE
)
errF
<-
learnErrors
(
snakemake
@
input
[[
1
]],
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
errR
<-
learnErrors
(
snakemake
@
input
[[
2
]],
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
dadaFs
<-
dada
(
derep
,
err
=
errF
,
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
dadaRs
<-
dada
(
derep
,
err
=
errR
,
multithread
=
snakemake
@
threads
,
verbose
=
TRUE
)
mergers
<-
mergePairs
(
dadaFs
,
dadaRs
,
verbose
=
TRUE
)
saveRDS
(
dada
,
snakemake
@
output
[[
1
]])
dada2.smk
View file @
7e4d83e6
rule dada2:
input:
"work/filter/{sample}.fastq.gz"
filt = "work/filter/{sample}_1.fastq.gz"
filtrev = "work/filter/{sample}_2.fastq.gz"
output:
"work/dada/{sample}.rds"
threads:
...
...
filterAndTrim.R
View file @
7e4d83e6
library
(
dada2
)
filterAndTrim
(
snakemake
@
input
[[
1
]],
snakemake
@
output
[[
1
]],
maxN
=
0
,
rm.phix
=
TRUE
,
compress
=
TRUE
,
verbose
=
TRUE
)
filterAndTrim
(
snakemake
@
input
[[
1
]],
snakemake
@
input
[[
2
]]
snakemake
@
output
[[
1
]],
maxN
=
0
,
rm.phix
=
TRUE
,
compress
=
TRUE
,
verbose
=
TRUE
)
global.smk
View file @
7e4d83e6
...
...
@@ -19,6 +19,7 @@ rule all:
"report/abundance.tsv",
# "report/tree.nwk"
include: "prefetech.smk"
include: "quality.smk"
include: "preprocess.smk"
include: "dada2.smk"
...
...
prefetech.smk
0 → 100644
View file @
7e4d83e6
rule prefetch:
output:
"DATA/.prefetch/{srr}.sra"
params:
"{srr} --max-size 50GB -O DATA"
log:
"DATA/.prefetch/sra/{srr}.log"
shell:
"conda activate sra-tools-2.10.1 "
"&& "
"prefetch {params} > {log} 2>&1 && touch {output} "
"&& "
"conda deactivate "
rule fastqdump:
input:
"DATA/.prefetch/{srr}.sra"
output:
touch("DATA/done__{srr}_dump")
params:
args = "-S -O DATA/ -t DATA/",
id_srr = "{srr}"
log:
"DATA/{srr}.log"
shell:
"conda activate sra-tools-2.10.1 "
"&& "
"fasterq-dump {params.args} {params.id_srr} > {log} 2>&1 "
"&& "
"conda deactivate "
\ No newline at end of file
preprocess.smk
View file @
7e4d83e6
rule cutadapt:
input:
"DATA/{sample}.fastq.gz"
fwd = "DATA/{sample}_1.fastq.gz"
rev = "DATA/{sample}_2.fastq.gz"
output:
"work/cutadapt/{sample}.fastq.gz"
cut = "work/cutadapt/{sample}_1.fastq.gz"
cutrev = "work/cutadapt/{sample}_2.fastq.gz"
params:
five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
...
...
@@ -22,8 +25,10 @@ rule cutadapt:
rule filter:
input:
"work/cutadapt/{sample}.fastq.gz"
cut = "work/cutadapt/{sample}_1.fastq.gz"
cutrev = "work/cutadapt/{sample}_2.fastq.gz"
output:
"work/filter/{sample}.fastq.gz"
filt = "work/filter/{sample}_1.fastq.gz"
filtrev = "work/filter/{sample}_2.fastq.gz"
script:
"filterAndTrim.R"
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