Commit 1a2c8a22 authored by Laura Denies's avatar Laura Denies
Browse files

make intermediate files temp

parent 97113017
...@@ -9,7 +9,7 @@ rule run_HMM_tox: ...@@ -9,7 +9,7 @@ rule run_HMM_tox:
hmm=config["pathofact"]["tox_hmm"], hmm=config["pathofact"]["tox_hmm"],
renamed="{datadir}/{project}/splitted/{sample}/{file_i}.fasta" renamed="{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/TOXIN/HMM_toxin/{sample}/{file_i}.log"
message: message:
...@@ -32,7 +32,7 @@ rule HMM_correct_format: ...@@ -32,7 +32,7 @@ rule HMM_correct_format:
input: input:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmmscan" "{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmmscan"
output: output:
"{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmm.csv" temp("{datadir}/{project}/TOXIN/HMM_toxin/{sample}/{file_i}.hmm.csv")
message: message:
"Adjust {input} to correct format: {output}" "Adjust {input} to correct format: {output}"
params: params:
......
...@@ -9,7 +9,7 @@ rule run_HMM_vir: ...@@ -9,7 +9,7 @@ rule run_HMM_vir:
hmm=config["pathofact"]["vir_hmm"], hmm=config["pathofact"]["vir_hmm"],
renamed="{datadir}/{project}/splitted/{sample}/{file_i}.fasta" renamed="{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/VIRULENCE/HMM_virulence/{sample}/{file_i}.log"
message: message:
...@@ -32,7 +32,7 @@ rule HMM_correct_format_vir: ...@@ -32,7 +32,7 @@ rule HMM_correct_format_vir:
input: input:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmmscan" "{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmmscan"
output: output:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmm.csv" temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}/{file_i}.hmm.csv")
message: message:
"Adjust {input} to correct format: {output}" "Adjust {input} to correct format: {output}"
params: params:
...@@ -76,7 +76,7 @@ rule HMM_R_VIR: ...@@ -76,7 +76,7 @@ rule HMM_R_VIR:
shared=config["pathofact"]["vir_domains"] + "/shared_domains.tsv", shared=config["pathofact"]["vir_domains"] + "/shared_domains.tsv",
ID="{datadir}/{project}/renamed/{sample}_translation.tsv" ID="{datadir}/{project}/renamed/{sample}_translation.tsv"
output: output:
"{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}/VIRULENCE/HMM_virulence/{sample}.hmm_results.log"
params: params:
...@@ -139,7 +139,7 @@ rule AAC: ...@@ -139,7 +139,7 @@ rule AAC:
input: input:
"{datadir}/{project}/splitted/{sample}/{file_i}.fasta" "{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/VIRULENCE/classifier_virulence/{sample}/{file_i}_AAC.log"
params: params:
...@@ -154,7 +154,7 @@ rule DPC: ...@@ -154,7 +154,7 @@ rule DPC:
input: input:
"{datadir}/{project}/splitted/{sample}/{file_i}.fasta" "{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/VIRULENCE/classifier_virulence/{sample}/{file_i}_DPC.log"
params: params:
...@@ -169,7 +169,7 @@ rule CTDC: ...@@ -169,7 +169,7 @@ rule CTDC:
input: input:
"{datadir}/{project}/splitted/{sample}/{file_i}.fasta" "{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDC.log"
params: params:
...@@ -184,7 +184,7 @@ rule CTDT: ...@@ -184,7 +184,7 @@ rule CTDT:
input: input:
"{datadir}/{project}/splitted/{sample}/{file_i}.fasta" "{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.log"
params: params:
...@@ -199,7 +199,7 @@ rule CTDD: ...@@ -199,7 +199,7 @@ rule CTDD:
input: input:
"{datadir}/{project}/splitted/{sample}/{file_i}.fasta" "{datadir}/{project}/splitted/{sample}/{file_i}.fasta"
output: output:
"{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}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.log"
params: params:
...@@ -218,7 +218,7 @@ rule join_matrix: ...@@ -218,7 +218,7 @@ rule join_matrix:
CTDT="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.txt", CTDT="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDT.txt",
CTDD="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.txt" CTDD="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_CTDD.txt"
output: output:
"{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_matrix.tsv" temp("{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_matrix.tsv")
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"]
...@@ -248,7 +248,7 @@ rule classifier: ...@@ -248,7 +248,7 @@ rule classifier:
input="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_matrix.tsv", input="{datadir}/{project}/VIRULENCE/classifier_virulence/{sample}/{file_i}_matrix.tsv",
model=config["pathofact"]["scripts"] + "/Virulence_factor_model.sav" model=config["pathofact"]["scripts"] + "/Virulence_factor_model.sav"
output: output:
"{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}/VIRULENCE/classifier_virulence/{sample}/{file_i}_classifier_prediction.log"
params: params:
......
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