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Johann Dreo
frictionlesser
Commits
f573af77
Commit
f573af77
authored
2 years ago
by
Johann Dreo
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refactor preprocessing
parent
1ad6cf88
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2 changed files
scripts/paris/config_preproc.yaml
+2
-2
2 additions, 2 deletions
scripts/paris/config_preproc.yaml
scripts/paris/preproc.Snakefile
+10
-15
10 additions, 15 deletions
scripts/paris/preproc.Snakefile
with
12 additions
and
17 deletions
scripts/paris/config_preproc.yaml
+
2
−
2
View file @
f573af77
snakefile
:
Snakefile
# executable: "singularity run ../../frictionlesser.sif"
executable
:
"
../../
release
/app/frictionlesser"
executable
:
"
../../
build
/app/frictionlesser"
cluster
:
"
sbatch
--job-name
{resources.job_name}
--mem
16G
--cpus-per-task=1
--partition
common,dedicated
--qos
fast
--output
logs/%j.out
--error
logs/%j.err"
cluster
:
"
sbatch
--job-name
{resources.job_name}
--mem
16G
--cpus-per-task=1
--partition
common,dedicated
--qos
fast
--output
data/inter/
logs/%j.out
--error
data/inter/
logs/%j.err"
sizes
:
-
10
...
...
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scripts/paris/preproc.Snakefile
+
10
−
15
View file @
f573af77
import datetime
configfile: "config.yaml"
# NOW=datetime.date.today().isoformat()
# workdir: "expe_{name}_{date}".format(name=config["expe-name"], date=NOW)
SEEDS=list(range(0,config["runs"]))
configfile: "config_preproc.yaml"
FRICTIONLESSER=config["executable"]
...
...
@@ -17,17 +12,17 @@ rule all:
rule preprocessing:
input:
counts="data/input/
2022_02_18_version_2_EOC_
counts.npz",
features="data/input/
2022_02_18_version_2_EOC_
features.csv",
meta="data/input/
2022_02_18_version_2_EOC_m
eta.csv"
counts="data/input/counts.npz",
features="data/input/features.csv",
meta="data/input/eta.csv"
output:
"data/inter/
2022_02_18_version_2_EOC_
counts.mara.hdf5"
"data/inter/counts.mara.hdf5"
shell:
"python3 preproc-mara__npz-to-hdf5.py {input.counts} {input.features} {input.meta}"
rule counts:
input:
"data/inter/
2022_02_18_version_2_EOC_
counts.mara.hdf5"
"data/inter/counts.mara.hdf5"
output:
"data/inter/counts.csv"
shell:
...
...
@@ -46,8 +41,8 @@ rule save_cache_transcriptome:
"data/inter/ranks.tsv"
output:
protected("cache/trans.cache.dat")
log: "logs/save_cache_transcriptome.log"
benchmark: "logs/save_cache_transcriptome.bench"
log: "
data/inter/
logs/save_cache_transcriptome.log"
benchmark: "
data/inter/
logs/save_cache_transcriptome.bench"
shell:
"{FRICTIONLESSER}"
" --ranks={input}"
...
...
@@ -64,8 +59,8 @@ rule save_cache_size:
wildcard_constraints:
# Wildcard {size} should be numeric.
size="\d+"
log: "logs/save_cache_size-{size}.log"
benchmark: "logs/save_cache_size-{size}.bench"
log: "
data/inter/
logs/save_cache_size-{size}.log"
benchmark: "
data/inter/
logs/save_cache_size-{size}.bench"
resources:
job_name=lambda wildcards: f"cache_z{wildcards.size}"
shell:
...
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