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Commit 037108b1 authored by Laura Denies's avatar Laura Denies
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limit nr. of files

parent c179d533
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config.yaml
View file @ 037108b1
pathofact:
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
workflow: "complete"
size_fasta: 100
......
rules/AMR/AMR.smk
View file @ 037108b1
......@@ -14,7 +14,7 @@ rule run_deepARG:
output:
temp("{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG")
log:
"{datadir}/{project}/AMR/deepARG_results/{sample}/{file_i}.out.mapping.ARG.log"
"{datadir}/{project}/AMR/logs/{sample}/{file_i}.out.mapping.ARG.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["medium"],
......@@ -55,7 +55,7 @@ rule run_RGI:
output:
temp("{datadir}/{project}/AMR/RGI_results/{sample}/{file_i}.RGI.txt")
log:
"{datadir}/{project}/AMR/RGI_results/{sample}/{file_i}.RGI.log"
"{datadir}/{project}/logs/{sample}/{file_i}.RGI.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["medium"],
......@@ -99,7 +99,7 @@ rule combine_AMR:
output:
AMR_combined="{datadir}/{project}/AMR/{sample}_AMR_prediction.tsv"
log:
"{datadir}/{project}/AMR/{sample}_combine_AMR_temp.log"
"{datadir}/{project}/logs/{sample}_combine_AMR_temp.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
......
rules/AMR/Combine_MGE_AMR.smk
View file @ 037108b1
......@@ -21,7 +21,7 @@ rule combine_AMR_plasmid:
Report_1="{datadir}/{project}/AMR/{sample}_AMR_MGE_prediction_detailed.tsv",
Report_2="{datadir}/{project}/AMR_MGE_prediction_{sample}_report.tsv"
log:
"{datadir}/{project}/AMR/{sample}_MGE_AMR_prediction_detail_temp.log"
"{datadir}/{project}/logs/{sample}_MGE_AMR_prediction_detail_temp.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["medium"],
......
rules/AMR/Phage.smk
View file @ 037108b1
......@@ -13,9 +13,9 @@ rule run_VirSorter:
input:
"{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
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:
"{datadir}/{project}/MGE/phage/{sample}/virsorter/VIRSorter_global-phage-signal.log"
"{datadir}/{project}/logs/{sample}/VIRSorter_global-phage-signal.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"],
......@@ -54,9 +54,9 @@ rule run_VirFinder:
input:
"{datadir}/{project}/contig_splitted/{sample}/{file_i}.fasta"
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:
"{datadir}/{project}/MGE/phage/{sample}/virfinder/{file_i}.fasta_gt1bp_dvfpred.log"
"{datadir}/{project}/logs/{sample}/{file_i}.fasta_gt1bp_dvfpred.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"],
......
rules/AMR/Plasmid.smk
View file @ 037108b1
......@@ -12,9 +12,9 @@ rule filter_seq:
input:
"{datadir}/{project}/renamed/{sample}_Contig_ID.fna"
output:
"{datadir}/{project}/{sample}_filtered.fna"
temp("{datadir}/{project}/plasmid/{sample}_filtered.fna")
log:
"{datadir}/{project}/{sample}_filtered.log"
"{datadir}/{project}/logs/{sample}_filtered.log"
conda:
"../../envs/Biopython.yaml"
params:
......@@ -28,7 +28,7 @@ rule filter_seq:
checkpoint splitplasmid:
input:
"{datadir}/{project}/{sample}_filtered.fna"
"{datadir}/{project}/plasmid/{sample}_filtered.fna"
output:
split=directory("{datadir}/{project}/MGE/plasmid_splitted/{sample}/")
params:
......@@ -50,7 +50,7 @@ rule run_PLASMID:
output:
temp("{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.tsv")
log:
"{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_plasflow_prediction.log"
"{datadir}/{project}/logs/{sample}/{file_i}_plasflow_prediction.log"
conda:
"../../envs/PlasFlow.yaml"
params:
......@@ -78,7 +78,7 @@ rule Plasmid_aggregate:
input:
aggregate_plasmid_input
output:
"{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_aggregated.tsv"
temp("{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}_plasflow_aggregated.tsv")
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
......@@ -106,7 +106,7 @@ rule run_MOBsuite:
output:
temp("{datadir}/{project}/MGE/plasmid/MOB_suite/{sample}/{file_i}_MOB_suite_prediction.txt")
log:
"{datadir}/{project}/MGE/plasmid/PlasFlow/{sample}/{file_i}_MOB_suite_prediction.log"
"{datadir}/{project}/logs/{sample}/{file_i}_MOB_suite_prediction.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"]
......
rules/Toxin/Combine_Toxin_SignalP.smk
View file @ 037108b1
......@@ -18,7 +18,7 @@ rule R_script:
gene_library="{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
gene_toxic="{datadir}/{project}/Toxin_prediction_{sample}_report.tsv"
log:
"{datadir}/{project}/TOXIN/R_output/{sample}_gene_table_library.log"
"{datadir}/{project}/logs/{sample}_gene_table_library.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
......
rules/Toxin/Toxin.smk
View file @ 037108b1
......@@ -11,7 +11,7 @@ rule run_HMM_tox:
output:
temp("{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmmscan")
log:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.log"
"{datadir}/{project}/logs/{sample}/{file_i}.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["long"],
......@@ -71,7 +71,7 @@ rule HMM_correct_format_3:
input:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R_temp.csv"
output:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R.csv"
temp("{datadir}/{project}/TOXIN/HMM_toxin/{sample}.Input_HMM_R.csv")
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
......
rules/Toxin/Toxin_report.smk
View file @ 037108b1
......@@ -18,7 +18,7 @@ rule R_script:
gene_library="{datadir}/{project}/Toxin_gene_library_{sample}_report.tsv",
gene_toxic="{datadir}/{project}/Toxin_prediction_{sample}_report.tsv"
log:
"{datadir}/{project}/TOXIN/R_output/{sample}_gene_table_library.log"
"{datadir}/{project}/logs/{sample}_gene_table_library.log"
message:
"Run external R script to join SignalP and ToxinHMM and create Toxin report (incl. confidence levels)"
params:
......
rules/Universal/Preprocessing.smk
View file @ 037108b1
......@@ -19,9 +19,11 @@ rule Prodigal:
outdir="{datadir}"
conda:
"../../envs/Prodigal.yaml"
log:
"{datadir}/{project}/logs/Prodigal_{sample}.log"
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}
"""
......@@ -92,7 +94,7 @@ checkpoint splitting:
output:
splits=directory("{datadir}/{project}/splitted/{sample}/")
log:
"{datadir}/{project}/splitted/{sample}.log"
"{datadir}/{project}/logs/split_ORF_{sample}.log"
params:
outdir="{datadir}",
runtime=config["pathofact"]["runtime"]["short"],
......@@ -102,5 +104,5 @@ checkpoint splitting:
"../../envs/Biopython.yaml"
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:
split=config["pathofact"]["size_fasta"]
conda:
"../../envs/Biopython.yaml"
log:
"{datadir}/{project}/logs/split_contig_{sample}.log"
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:
output:
Virulence_report="{datadir}/{project}/Virulence_prediction_{sample}_report.tsv"
log:
"{datadir}/{project}/VIRULENCE//{sample}.combine_virulence_results.log"
"{datadir}/{project}/logs/{sample}.combine_virulence_results.log"
params:
runtime=config["pathofact"]["runtime"]["short"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......
rules/Virulence/Virulence.smk
View file @ 037108b1
......@@ -11,7 +11,7 @@ rule run_HMM_vir:
output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmmscan")
log:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.log"
"{datadir}/{project}/logs/{sample}/{file_i}.log"
message:
"Run HMM scan on {input.renamed} to generate {output}"
params:
......@@ -60,7 +60,7 @@ rule HMM_correct_format_2_vir:
input:
aggregate_hmm
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}"
params:
outdir="{datadir}",
......@@ -81,7 +81,7 @@ rule HMM_R_VIR:
output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv")
log:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.log"
"{datadir}/{project}/logs/{sample}.hmm_results.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......@@ -145,7 +145,7 @@ rule AAC:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_AAC.txt")
log:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_AAC.log"
"{datadir}/{project}/logs/{sample}/{file_i}_AAC.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......@@ -161,7 +161,7 @@ rule DPC:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_DPC.txt")
log:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_DPC.log"
"{datadir}/{project}/logs/{sample}/{file_i}_DPC.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......@@ -177,7 +177,7 @@ rule CTDC:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDC.txt")
log:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDC.log"
"{datadir}/{project}/logs/{sample}/{file_i}_CTDC.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......@@ -193,7 +193,7 @@ rule CTDT:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.txt")
log:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.log"
"{datadir}/{project}/logs/{sample}/{file_i}_CTDT.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......@@ -209,7 +209,7 @@ rule CTDD:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.txt")
log:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.log"
"{datadir}/{project}/logs/{sample}/{file_i}_CTDD.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......@@ -260,7 +260,7 @@ rule classifier:
output:
temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_classifier_prediction.tsv")
log:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_classifier_prediction.log"
"{datadir}/{project}/logs/{sample}/{file_i}_classifier_prediction.log"
params:
runtime=config["pathofact"]["runtime"]["medium"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
......
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