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Laura Denies
PathoFact
Commits
037108b1
Commit
037108b1
authored
Jul 22, 2020
by
Laura Denies
Browse files
limit nr. of files
parent
c179d533
Changes
12
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config.yaml
View file @
037108b1
pathofact
:
pathofact
:
sample
:
[
"
test_2"
]
# requires user input
sample
:
[
"
test_2"
]
# requires user input
project
:
PathoFact
_test_2
# requires user input
project
:
Lim_
PathoFact
# requires user input
datadir
:
../test_dataset
# requires user input
datadir
:
../test_dataset
# requires user input
workflow
:
"
complete"
workflow
:
"
complete"
size_fasta
:
100
size_fasta
:
100
...
...
rules/AMR/AMR.smk
View file @
037108b1
...
@@ -14,7 +14,7 @@ rule run_deepARG:
...
@@ -14,7 +14,7 @@ rule run_deepARG:
output:
output:
temp("{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG")
temp("{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG")
log:
log:
"{datadir}/{project}/AMR/
deepARG_result
s/{sample}/{file_i}.out.mapping.ARG.log"
"{datadir}/{project}/AMR/
log
s/{sample}/{file_i}.out.mapping.ARG.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
...
@@ -55,7 +55,7 @@ rule run_RGI:
...
@@ -55,7 +55,7 @@ rule run_RGI:
output:
output:
temp("{datadir}/{project}/AMR/RGI_results/{sample}/{file_i}.RGI.txt")
temp("{datadir}/{project}/AMR/RGI_results/{sample}/{file_i}.RGI.txt")
log:
log:
"{datadir}/{project}/
AMR/RGI_result
s/{sample}/{file_i}.RGI.log"
"{datadir}/{project}/
log
s/{sample}/{file_i}.RGI.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
...
@@ -99,7 +99,7 @@ rule combine_AMR:
...
@@ -99,7 +99,7 @@ rule combine_AMR:
output:
output:
AMR_combined="{datadir}/{project}/AMR/{sample}_AMR_prediction.tsv"
AMR_combined="{datadir}/{project}/AMR/{sample}_AMR_prediction.tsv"
log:
log:
"{datadir}/{project}/
AMR
/{sample}_combine_AMR_temp.log"
"{datadir}/{project}/
logs
/{sample}_combine_AMR_temp.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
runtime=config["pathofact"]["runtime"]["short"],
...
...
rules/AMR/Combine_MGE_AMR.smk
View file @
037108b1
...
@@ -21,7 +21,7 @@ rule combine_AMR_plasmid:
...
@@ -21,7 +21,7 @@ rule combine_AMR_plasmid:
Report_1="{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv",
Report_1="{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv",
Report_2="{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv"
Report_2="{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv"
log:
log:
"{datadir}/{project}/
AMR
/{sample}_MGE_AMR_prediction_detail_temp.log"
"{datadir}/{project}/
logs
/{sample}_MGE_AMR_prediction_detail_temp.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
...
...
rules/AMR/Phage.smk
View file @
037108b1
...
@@ -13,9 +13,9 @@ rule run_VirSorter:
...
@@ -13,9 +13,9 @@ rule run_VirSorter:
input:
input:
"{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
"{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
output:
output:
"{datadir}/{project}/MGE/phage/{sample}/virsorter/VIRSorter_global-phage-signal.csv"
temp(
"{datadir}/{project}/MGE/phage/{sample}/virsorter/VIRSorter_global-phage-signal.csv"
)
log:
log:
"{datadir}/{project}/
MGE/phage/{sample}/virsorter
/VIRSorter_global-phage-signal.log"
"{datadir}/{project}/
logs/{sample}
/VIRSorter_global-phage-signal.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"],
runtime=config["pathofact"]["runtime"]["long"],
...
@@ -54,9 +54,9 @@ rule run_VirFinder:
...
@@ -54,9 +54,9 @@ rule run_VirFinder:
input:
input:
"{datadir}/{project}/contig_splitted/{sample}/{file_i}.fasta"
"{datadir}/{project}/contig_splitted/{sample}/{file_i}.fasta"
output:
output:
"{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fasta_gt1bp_dvfpred.txt"
temp(
"{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fasta_gt1bp_dvfpred.txt"
)
log:
log:
"{datadir}/{project}/
MGE/phage/{sample}/virfinder
/{file_i}.fasta_gt1bp_dvfpred.log"
"{datadir}/{project}/
logs/{sample}
/{file_i}.fasta_gt1bp_dvfpred.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"],
runtime=config["pathofact"]["runtime"]["long"],
...
...
rules/AMR/Plasmid.smk
View file @
037108b1
...
@@ -12,9 +12,9 @@ rule filter_seq:
...
@@ -12,9 +12,9 @@ rule filter_seq:
input:
input:
"{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
"{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
output:
output:
"{datadir}/{project}/{sample}_filtered.fna"
temp(
"{datadir}/{project}/
plasmid/
{sample}_filtered.fna"
)
log:
log:
"{datadir}/{project}/{sample}_filtered.log"
"{datadir}/{project}/
logs/
{sample}_filtered.log"
conda:
conda:
"../../envs/Biopython.yaml"
"../../envs/Biopython.yaml"
params:
params:
...
@@ -28,7 +28,7 @@ rule filter_seq:
...
@@ -28,7 +28,7 @@ rule filter_seq:
checkpoint splitplasmid:
checkpoint splitplasmid:
input:
input:
"{datadir}/{project}/{sample}_filtered.fna"
"{datadir}/{project}/
plasmid/
{sample}_filtered.fna"
output:
output:
split=directory("{datadir}/{project}/MGE/plasmid_splitted/{sample}/")
split=directory("{datadir}/{project}/MGE/plasmid_splitted/{sample}/")
params:
params:
...
@@ -50,7 +50,7 @@ rule run_PLASMID:
...
@@ -50,7 +50,7 @@ rule run_PLASMID:
output:
output:
temp("{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.tsv")
temp("{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.tsv")
log:
log:
"{datadir}/{project}/
MGE/plasmid/PlasFlow
/{sample}/{file_i}_plasflow_prediction.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_plasflow_prediction.log"
conda:
conda:
"../../envs/PlasFlow.yaml"
"../../envs/PlasFlow.yaml"
params:
params:
...
@@ -78,7 +78,7 @@ rule Plasmid_aggregate:
...
@@ -78,7 +78,7 @@ rule Plasmid_aggregate:
input:
input:
aggregate_plasmid_input
aggregate_plasmid_input
output:
output:
"{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_aggregated.tsv"
temp(
"{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_aggregated.tsv"
)
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
runtime=config["pathofact"]["runtime"]["short"],
...
@@ -106,7 +106,7 @@ rule run_MOBsuite:
...
@@ -106,7 +106,7 @@ rule run_MOBsuite:
output:
output:
temp("{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}/{file_i}_MOB_suite_prediction.txt")
temp("{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}/{file_i}_MOB_suite_prediction.txt")
log:
log:
"{datadir}/{project}/
MGE/plasmid/PlasFlow
/{sample}/{file_i}_MOB_suite_prediction.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_MOB_suite_prediction.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"]
runtime=config["pathofact"]["runtime"]["long"]
...
...
rules/Toxin/Combine_Toxin_SignalP.smk
View file @
037108b1
...
@@ -18,7 +18,7 @@ rule R_script:
...
@@ -18,7 +18,7 @@ rule R_script:
gene_library="{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
gene_library="{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
gene_toxic="{datadir}/{project}/Toxin_prediction_{sample}_report.tsv"
gene_toxic="{datadir}/{project}/Toxin_prediction_{sample}_report.tsv"
log:
log:
"{datadir}/{project}/
TOXIN/R_output
/{sample}_gene_table_library.log"
"{datadir}/{project}/
logs
/{sample}_gene_table_library.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
runtime=config["pathofact"]["runtime"]["short"],
...
...
rules/Toxin/Toxin.smk
View file @
037108b1
...
@@ -11,7 +11,7 @@ rule run_HMM_tox:
...
@@ -11,7 +11,7 @@ rule run_HMM_tox:
output:
output:
temp("{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmmscan")
temp("{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmmscan")
log:
log:
"{datadir}/{project}/
TOXIN/HMM_toxin
/{sample}/{file_i}.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"],
runtime=config["pathofact"]["runtime"]["long"],
...
@@ -71,7 +71,7 @@ rule HMM_correct_format_3:
...
@@ -71,7 +71,7 @@ rule HMM_correct_format_3:
input:
input:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R_temp.csv"
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R_temp.csv"
output:
output:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R.csv"
temp(
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R.csv"
)
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
runtime=config["pathofact"]["runtime"]["short"],
...
...
rules/Toxin/Toxin_report.smk
View file @
037108b1
...
@@ -18,7 +18,7 @@ rule R_script:
...
@@ -18,7 +18,7 @@ rule R_script:
gene_library="{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
gene_library="{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
gene_toxic="{datadir}/{project}/Toxin_prediction_{sample}_report.tsv"
gene_toxic="{datadir}/{project}/Toxin_prediction_{sample}_report.tsv"
log:
log:
"{datadir}/{project}/
TOXIN/R_output
/{sample}_gene_table_library.log"
"{datadir}/{project}/
logs
/{sample}_gene_table_library.log"
message:
message:
"Run external R script to join SignalP and ToxinHMM and create Toxin report (incl. confidence levels)"
"Run external R script to join SignalP and ToxinHMM and create Toxin report (incl. confidence levels)"
params:
params:
...
...
rules/Universal/Preprocessing.smk
View file @
037108b1
...
@@ -19,9 +19,11 @@ rule Prodigal:
...
@@ -19,9 +19,11 @@ rule Prodigal:
outdir="{datadir}"
outdir="{datadir}"
conda:
conda:
"../../envs/Prodigal.yaml"
"../../envs/Prodigal.yaml"
log:
"{datadir}/{project}/logs/Prodigal_{sample}.log"
shell:
shell:
"""
"""
prodigal -i {input} -o {output.GFF} -a {output.ORF} -f gff -p meta
prodigal -i {input} -o {output.GFF} -a {output.ORF} -f gff -p meta
&> {log}
sed -i 's/[^>]*ID=//;s/;.*//;s/*//' {output.ORF}
sed -i 's/[^>]*ID=//;s/;.*//;s/*//' {output.ORF}
"""
"""
...
@@ -92,7 +94,7 @@ checkpoint splitting:
...
@@ -92,7 +94,7 @@ checkpoint splitting:
output:
output:
splits=directory("{datadir}/{project}/splitted/{sample}/")
splits=directory("{datadir}/{project}/splitted/{sample}/")
log:
log:
"{datadir}/{project}/
splitted/
{sample}.log"
"{datadir}/{project}/
logs/split_ORF_
{sample}.log"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
runtime=config["pathofact"]["runtime"]["short"],
...
@@ -102,5 +104,5 @@ checkpoint splitting:
...
@@ -102,5 +104,5 @@ checkpoint splitting:
"../../envs/Biopython.yaml"
"../../envs/Biopython.yaml"
shell:
shell:
"""
"""
python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/splitted/{wildcards.sample}
python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/splitted/{wildcards.sample}
&> {log}
"""
"""
rules/Universal/Preprocessing_contig.smk
View file @
037108b1
...
@@ -54,9 +54,11 @@ checkpoint splitcontig:
...
@@ -54,9 +54,11 @@ checkpoint splitcontig:
split=config["pathofact"]["size_fasta"]
split=config["pathofact"]["size_fasta"]
conda:
conda:
"../../envs/Biopython.yaml"
"../../envs/Biopython.yaml"
log:
"{datadir}/{project}/logs/split_contig_{sample}.log"
shell:
shell:
"""
"""
python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/contig_splitted/{wildcards.sample}
python {config[pathofact][scripts]}/split.py {input} {params.split} {wildcards.datadir}/{wildcards.project}/contig_splitted/{wildcards.sample}
&> {log}
"""
"""
rules/Virulence/Combine_Virulence_SignalP.smk
View file @
037108b1
...
@@ -16,7 +16,7 @@ rule merge_SignalPVir:
...
@@ -16,7 +16,7 @@ rule merge_SignalPVir:
output:
output:
Virulence_report="{datadir}/{project}/Virulence_prediction_{sample}_report.tsv"
Virulence_report="{datadir}/{project}/Virulence_prediction_{sample}_report.tsv"
log:
log:
"{datadir}/{project}/
VIRULENCE/
/{sample}.combine_virulence_results.log"
"{datadir}/{project}/
logs
/{sample}.combine_virulence_results.log"
params:
params:
runtime=config["pathofact"]["runtime"]["short"],
runtime=config["pathofact"]["runtime"]["short"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
...
rules/Virulence/Virulence.smk
View file @
037108b1
...
@@ -11,7 +11,7 @@ rule run_HMM_vir:
...
@@ -11,7 +11,7 @@ rule run_HMM_vir:
output:
output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmmscan")
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmmscan")
log:
log:
"{datadir}/{project}/
VIRULENCE/HMM_virulence
/{sample}/{file_i}.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}.log"
message:
message:
"Run HMM scan on {input.renamed} to generate {output}"
"Run HMM scan on {input.renamed} to generate {output}"
params:
params:
...
@@ -60,7 +60,7 @@ rule HMM_correct_format_2_vir:
...
@@ -60,7 +60,7 @@ rule HMM_correct_format_2_vir:
input:
input:
aggregate_hmm
aggregate_hmm
output:
output:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.Input_HMM_R.csv"
temp(
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.Input_HMM_R.csv"
)
message: "Aggregate virulence factor prediction (HMM) on the following sample(s): {wildcards.project} - {wildcards.sample}"
message: "Aggregate virulence factor prediction (HMM) on the following sample(s): {wildcards.project} - {wildcards.sample}"
params:
params:
outdir="{datadir}",
outdir="{datadir}",
...
@@ -81,7 +81,7 @@ rule HMM_R_VIR:
...
@@ -81,7 +81,7 @@ rule HMM_R_VIR:
output:
output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv")
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv")
log:
log:
"{datadir}/{project}/
VIRULENCE/HMM_virulence
/{sample}.hmm_results.log"
"{datadir}/{project}/
logs
/{sample}.hmm_results.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
@@ -145,7 +145,7 @@ rule AAC:
...
@@ -145,7 +145,7 @@ rule AAC:
output:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_AAC.txt")
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_AAC.txt")
log:
log:
"{datadir}/{project}/
VIRULENCE/classifier_virulence
/{sample}/{file_i}_AAC.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_AAC.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
@@ -161,7 +161,7 @@ rule DPC:
...
@@ -161,7 +161,7 @@ rule DPC:
output:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_DPC.txt")
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_DPC.txt")
log:
log:
"{datadir}/{project}/
VIRULENCE/classifier_virulence
/{sample}/{file_i}_DPC.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_DPC.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
@@ -177,7 +177,7 @@ rule CTDC:
...
@@ -177,7 +177,7 @@ rule CTDC:
output:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDC.txt")
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDC.txt")
log:
log:
"{datadir}/{project}/
VIRULENCE/classifier_virulence
/{sample}/{file_i}_CTDC.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_CTDC.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
@@ -193,7 +193,7 @@ rule CTDT:
...
@@ -193,7 +193,7 @@ rule CTDT:
output:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.txt")
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.txt")
log:
log:
"{datadir}/{project}/
VIRULENCE/classifier_virulence
/{sample}/{file_i}_CTDT.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_CTDT.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
@@ -209,7 +209,7 @@ rule CTDD:
...
@@ -209,7 +209,7 @@ rule CTDD:
output:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.txt")
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.txt")
log:
log:
"{datadir}/{project}/
VIRULENCE/classifier_virulence
/{sample}/{file_i}_CTDD.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_CTDD.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
@@ -260,7 +260,7 @@ rule classifier:
...
@@ -260,7 +260,7 @@ rule classifier:
output:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_classifier_prediction.tsv")
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_classifier_prediction.tsv")
log:
log:
"{datadir}/{project}/
VIRULENCE/classifier_virulence
/{sample}/{file_i}_classifier_prediction.log"
"{datadir}/{project}/
logs
/{sample}/{file_i}_classifier_prediction.log"
params:
params:
runtime=config["pathofact"]["runtime"]["medium"],
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
...
...
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