diff --git a/scripts/paris/config_preproc.yaml b/scripts/paris/config_preproc.yaml index beb2afa5217d90f112a4ac69079b9e3ccd106ca8..32b00759ca8b005bce26c8eee6fda32c403931dd 100644 --- a/scripts/paris/config_preproc.yaml +++ b/scripts/paris/config_preproc.yaml @@ -1,9 +1,9 @@ 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 diff --git a/scripts/paris/preproc.Snakefile b/scripts/paris/preproc.Snakefile index 23eeafb857841c4b2196ac8db54d25df8cd683e7..f5805119416e46ca385cf4836217dcf22b419a3c 100644 --- a/scripts/paris/preproc.Snakefile +++ b/scripts/paris/preproc.Snakefile @@ -1,11 +1,6 @@ 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_meta.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: