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