Commit 33756c49 authored by Valentina Galata's avatar Valentina Galata
Browse files

adjusted paths to scripts in rules (issue #15)

parent 27eb51b0
......@@ -26,7 +26,7 @@ rule combine_AMR_plasmid:
Report_2=temp("{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_report_temp.csv")
params: outdir="{OUTDIR}"
conda: "../../envs/R.yaml"
script: "AMR_MGE.R"
script: "../../scripts/AMR_MGE.R"
rule modify_details:
input:"{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_detail_temp.csv"
......
......@@ -24,7 +24,7 @@ rule R_script:
message: "Run external R script to join SignalP and ToxinHMM"
params: outdir="{OUTDIR}"
conda: "../../envs/R.yaml"
script: "ownHMM_library.R"
script: "../../scripts/ownHMM_library.R"
#Put the different files in the correct configuration
###Gene table library
......
......@@ -14,7 +14,7 @@ rule combine_PathoFact:
AMR_MGE="{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv"
output: "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
conda: "../../envs/R.yaml"
script: "PathoFact.R"
script: "../../scripts/PathoFact.R"
......@@ -56,7 +56,7 @@ rule HMM_R_VIR:
ID="{OUTDIR}/{project}/renamed/{input_file}_translation.tsv"
output: "{OUTDIR}/{project}/VIRULENCE/HMM_virulence/{input_file}.hmm_results.csv"
conda: "../../envs/R.yaml"
script: "hmm.R"
script: "../../scripts/hmm.R"
## Give pathogenicity prediction
......
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