Commit 0af29a75 authored by ahb-ufz's avatar ahb-ufz
Browse files

always use getThreads

parent 67855431
......@@ -16,7 +16,7 @@ rule mapping_on_assembly:
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/assembly_mapping_on_assembly.{type}.log"
message: "mapping_on_assembly: Mapping {wildcards.type} reads on merged assembly."
......
......@@ -29,7 +29,7 @@ rule megahit_assembly_from_preprocessing:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_megahit_assembly_from_preprocessing.{type}.log"
message: "megahit_assembly_from_preprocessing: Performing {wildcards.type} assembly step 1 from preprocessed reads using MEGAHIT"
......@@ -48,7 +48,7 @@ rule megahit_assembly_from_unmapped:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_megahit_assembly_from_unmapped.{type}.log"
message: "megahit_assembly_from_unmapped: Performing {wildcards.type} assembly step 2 from unmapped reads using MEGAHIT"
......
......@@ -79,7 +79,7 @@ elif config["assembly"]["merge"] == "flye":
sample = SAMPLE,
iters = 0,
minoverlap = 1000
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda:
os.path.join(ENVDIR, "IMP_assembly.yaml")
log:
......
......@@ -33,7 +33,7 @@ if LONG:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_assembly_from_preprocessing.{type}.log"
message: "metaspades_assembly_from_preprocessing: Performing {wildcards.type} assembly step 1 from preprocessed reads using MetaSpades"
......@@ -52,7 +52,7 @@ else:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_assembly_from_preprocessing.{type}.log"
message: "metaspades_assembly_from_preprocessing: Performing {wildcards.type} assembly step 1 from preprocessed reads using MetaSpades"
......@@ -71,7 +71,7 @@ rule metaspades_assembly_from_unmapped:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_assembly_from_unmapped.{type}.log"
message: "metaspades_assembly_from_unmapped: Performing {wildcards.type} assembly step 2 from unmapped reads using METASPADES"
......
......@@ -41,7 +41,7 @@ rule extract_unmapped_from_megahit:
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/assembly_extract_unmapped_from_megahit.{type}.log"
message: "extract_unmapped_from_megahit: Extracting unmapped {wildcards.type} reads from megahit assembly."
......@@ -66,7 +66,7 @@ rule extract_unmapped_from_hybrid_assembly:
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/assembly_extract_unmapped_from_hybrid_assembly.{assembler}.{type}.log"
message: "extract_unmapped_from_hybrid_assembly: Extracting unmapped {wildcards.type} reads from hybrid {wildcards.assembler} assembly."
......
......@@ -15,7 +15,7 @@ rule megahit_hybrid_assembly_1:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_megahit_hybrid_assembly_1.log"
message: "megahit_hybrid_assembly_1: Performing hybrid assembly 1 from preprocessed reads using MEGAHIT"
......@@ -53,7 +53,7 @@ rule megahit_hybrid_assembly_2:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_megahit_hybrid_assembly_2.log"
message: "megahit_hybrid_assembly_2: Performing hybrid assembly 2 from preprocessed reads using MEGAHIT"
......
......@@ -79,7 +79,7 @@ elif config["assembly"]["merge"] == "flye":
sample = SAMPLE,
iters = 0,
minoverlap = 1000
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda:
os.path.join(ENVDIR, "IMP_assembly.yaml")
log:
......
......@@ -43,7 +43,7 @@ else:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_hybrid_assembly_1.log"
message: "metaspades_hybrid_assembly_1: Performing hybrid assembly 1 from preprocessed reads using METASPADES"
......@@ -72,7 +72,7 @@ rule metaspades_hybrid_assembly_2:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_hybrid_assembly_2.log"
message: "metaspades_hybrid_assembly_2: Performing hybrid assembly 2 from preprocessed reads using metaspades"
......
......@@ -44,7 +44,7 @@ rule extract_unmapped:
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/assembly_extract_unmapped.{type}.log"
message: "extract_unmapped: Extracting unmapped {wildcards.type} reads from megahit assembly."
......
......@@ -34,7 +34,7 @@ rule metaspades_assembly_from_preprocessing:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_assembly_from_preprocessing.mt.log"
message: "metaspades_assembly_from_preprocessing: Performing mt assembly step 1 from preprocessed reads using MetaSpades"
......@@ -53,7 +53,7 @@ rule metaspades_assembly_from_unmapped:
resources:
runtime = "120:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_assembly.yaml"
log: "logs/assembly_metaspades_assembly_from_unmapped.mt.log"
message: "metaspades_assembly_from_unmapped: Performing mt assembly step 2 from unmapped reads using METASPADES"
......
......@@ -17,7 +17,7 @@ rule DAS_tool:
"Binning/selected_DASTool_summary.txt",
"Binning/selected_DASTool_scaffolds2bin.txt",
directory("Binning/selected_DASTool_bins")
threads: 4
threads: getThreads(4)
resources:
runtime = "24:00:00",
mem = BIGMEMCORE
......
......@@ -61,7 +61,7 @@ rule cdhit:
"Catalogue/multi_prokka.ffn"
output:
"Catalogue/catalogue.fasta"
threads: BIGCORENO
threads: getThreads(BIGCORENO)
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
......
......@@ -11,7 +11,7 @@ rule kraken_cat:
resources:
runtime = "8:00:00",
mem = BIGMEMCORE
threads: KRAKTHREADS
threads: getThreads(KRAKTHREADS)
conda: ENVDIR + "/IMP_taxonomy.yaml"
log: "logs/analysis_kraken_cat"
message: "kraken_cat: Running kraken2 on genes from catalog against {config[catalogue][kraken][db]}."
......
......@@ -9,7 +9,7 @@ rule mapping_on_catalogue:
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/catalogue_mapping_on_catalogue.{type}.{sample}.log"
message: "mapping_on_catalogue: Mapping {wildcards.type} reads on catalogue."
......
......@@ -12,7 +12,7 @@ rule cross_mapping:
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/dereplicate_cross_mapping_{cross_sample}.on.{sample}.log"
message: "cross_mapping: Mapping {wildcards.cross_sample} reads on {wildcards.sample} contigs."
......
......@@ -18,7 +18,7 @@ checkpoint dRep_multi:
directory("Dereplication/dRep_multi_out/dereplicated_genomes"),
expand("Dereplication/dRep_multi_out/data_tables/{file}.csv",
file=["Chdb","Cdb","Sdb","Wdb","Widb","Ndb"])
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_multi.yaml"
resources:
runtime = "12:00:00",
......
......@@ -39,7 +39,7 @@ rule dRep_simple:
directory("Dereplication/dRep_single_out/dereplicated_genomes"),
expand("Dereplication/dRep_single_out/data_tables/{file}.csv",
file=["Chdb","Cdb","Sdb","Wdb","Widb","Ndb"])
threads: BIGCORENO
threads: getThreads(BIGCORENO)
resources:
runtime = "12:00:00",
mem = BIGMEMCORE
......
......@@ -11,7 +11,7 @@ rule GTDBtk_bins:
conda: ENVDIR + "/IMP_gtdbtk.yaml"
log: "logs/dereplication_GTDBtk_bins.{clusterID}.log"
message: "GTDBtk_bins: Classifiying {wildcards.clusterID} using GTDBtk."
threads: BIGCORENO
threads: getThreads(BIGCORENO)
shell:
"""
mkdir -p {params.outdir} && cp {input} {params.outdir}
......
......@@ -34,7 +34,7 @@ rule mg_filtering:
resources:
runtime = "8:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/preprocessing_mg_filtering.{filterstep}.log"
message: "mg_filtering: Filtering mg reads to get {wildcards.filterstep}."
......@@ -52,7 +52,7 @@ rule mt_filtering:
resources:
runtime = "8:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/preprocessing_mt_filtering.{filterstep}.log"
message: "mt_filtering: Filtering mt reads to get {wildcards.filterstep}."
......
......@@ -20,7 +20,7 @@ rule mg_filtering:
resources:
runtime = "24:00:00",
mem = BIGMEMCORE
threads: BIGCORENO
threads: getThreads(BIGCORENO)
conda: ENVDIR + "/IMP_mapping.yaml"
log: "logs/preprocessing_mg_filtering.{filterstep}.log"
message: "mg_filtering: Filtering mg reads to get {wildcards.filterstep}."
......
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