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edna
snakemake_only_obitools
Commits
2bbeb9a7
Commit
2bbeb9a7
authored
Dec 02, 2019
by
peguerin
Browse files
main snakemake command
parent
774ace31
Changes
1
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main.sh
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2bbeb9a7
# arguments
FOLDER_INPUT
=
$1
REFERENCE_BASE
=
$2
CORES
=
$3
# working folders
mkdir
-p
01-assembly 02-demultiplex 99-log runs tables
# link base reference
ln
-s
$REFERENCE_BASE
bdr
# link raw sequences data
for
i
in
`
ls
$FOLDER_INPUT
*
fastq.gz
`
;
do
name
=
`
basename
$i
`
;
ln
-s
$i
raw/
$name
;
done
# link barcode data
for
i
in
`
ls
$FOLDER_INPUT
*
dat
`
;
do
name
=
`
basename
$i
`
;
ln
-s
$i
barcodes/
$name
;
done
# run pipeline
snakemake
-s
scripts/step1.sf
-j
$CORES
--latency-wait
120
snakemake
-s
scripts/step2.sf
-j
$CORES
--latency-wait
120
snakemake
-s
scripts/step3.sf
-j
$CORES
--latency-wait
120
snakemake
-s
scripts/step4.sf
-j
$CORES
--latency-wait
120
## this work !
mkdir
-p
01-assembly 02-demultiplex/02-01-raw 02-demultiplex/02-02-filtered 02-demultiplex/02-03-cleaned 99-log 03-filtered
## assemble & demultiplex
cd
01-assembly
snakemake
-s
Snakefile
-j
8
--use-singularity
--singularity-args
"--bind /media/superdisk:/media/superdisk"
--latency-wait
120
cd
..
## filter sequences
cd
02-demultiplex
snakemake
-s
Snakefile
-j
8
--use-singularity
--singularity-args
"--bind /media/superdisk:/media/superdisk"
--latency-wait
120
snakemake
-s
Snakefile
-j
8
--dry-run
--use-singularity
--singularity-args
"--bind /media/superdisk:/media/superdisk"
--latency-wait
120
cd
..
## concatenate samples into run
for
run
in
`
ls
02-demultiplex/03-cleaned/
`
;
do
cat
02-demultiplex/03-cleaned/
${
run
}
/
*
.c.r.l.u.fasta
>
03-filtered/01-runs/
${
run
}
_run.fasta
;
done
## taxonomic assignation & format
cd
03-filtered
snakemake
-s
Snakefile
-j
8
--dry-run
--use-singularity
--singularity-args
"--bind /media/superdisk:/media/superdisk"
--latency-wait
120
cd
..
## clean
snakemake
-s
Snakefile
--delete-all-output
--dry-run
snakemake
-s
Snakefile
--delete-all-output
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