adjusted paths to YAML files in rules (issue #14)

rules/AMR/AMR

@@ -16,7 +16,7 @@ rule run_deepARG:
 	input:"{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
 	output:temp("{OUTDIR}/{project}/AMR/deepARG_results/{input_file}/{file_i}.out.mapping.ARG")
 	params: outdir="{OUTDIR}"
-	conda: "../../conda_environments/AMR.yml"
+	conda: "../../envs/DeepARG.yaml"
 	shell: "python {config[deep_ARG]} --align --type prot --genes --input {input} --output {wildcards.OUTDIR}/{wildcards.project}/AMR/deepARG_results/{wildcards.input_file}/{wildcards.file_i}.out"
 
 

rules/AMR/Combine_MGE_AMR

@@ -25,7 +25,7 @@ rule combine_AMR_plasmid:
 		Report_1=temp("{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_detail_temp.csv"),
 		Report_2=temp("{OUTDIR}/{project}/AMR/{input_file}_MGE_AMR_prediction_report_temp.csv")
 	params: outdir="{OUTDIR}"
-	conda: "../../conda_environments/renv.yaml"
+	conda: "../../envs/R.yaml"
 	script: "AMR_MGE.R"
 
 rule modify_details:

rules/AMR/Phage

@@ -18,7 +18,7 @@ checkpoint splitphage:
         input: "{OUTDIR}/{project}/renamed/{input_file}_Contig_ID.fna"
         output: split=directory("{OUTDIR}/{project}/contig_splitted/{input_file}/")
         params: outdir="{OUTDIR}"
-        conda: "../../conda_environments/Seqkit.yml"
+        conda: "../../envs/SeqKit.yaml"
         shell: """
                 seqkit split2 -s 10000 {input} -O {wildcards.OUTDIR}/{wildcards.project}/contig_splitted/{wildcards.input_file}
                 """
@@ -27,7 +27,7 @@ rule run_VirSorter:
 	input: "{OUTDIR}/{project}/renamed/{input_file}_Contig_ID.fna"
 	output: "{OUTDIR}/{project}/MGE/phage/{input_file}/virsorter/VIRSorter_global-phage-signal.csv"
 	params: outdir="{OUTDIR}"
-	conda: "../../conda_environments/virsorter.yml"
+	conda: "../../envs/VirSorter.yaml"
 	threads: 12
 	shell: """
 		{config[virsorter]} -f {input} --ncpu {threads} --wdir {wildcards.OUTDIR}/{wildcards.project}/MGE/phage/{wildcards.input_file}/virsorter --data-dir {config[virsorter_data]}
@@ -43,7 +43,7 @@ rule run_Virfinder:
         input: "{OUTDIR}/{project}/contig_splitted/{input_file}/{file_i}.fna"
         output: "{OUTDIR}/{project}/MGE/phage/{input_file}/virfinder/{file_i}.fna_gt1bp_dvfpred.txt"
         params: outdir="{OUTDIR}"
-	conda: "../../conda_environments/virfinder.yml"
+	conda: "../../envs/DeepVirFinder.yaml"
 	threads: 12
         shell: "python {config[DeepVirFinder]} -i {input} -o {wildcards.OUTDIR}/{wildcards.project}/MGE/phage/{wildcards.input_file}/virfinder -c {threads}"
 

rules/AMR/Plasmid

@@ -16,7 +16,7 @@ INPUT=config["input_file"]
 rule filter_seq:
         input: "{OUTDIR}/{project}/renamed/{input_file}_Contig_ID.fna"
         output: "{OUTDIR}/{project}/{input_file}_filtered.fna"
-        conda: "../../conda_environments/biopython_env.yaml"
+        conda: "../../envs/Biopython.yaml"
         params: outdir="{OUTDIR}"
         shell: "./scripts/filter.pl 1000 {input} > {output}"
 
@@ -24,7 +24,7 @@ checkpoint splitplasmid:
         input: "{OUTDIR}/{project}/{input_file}_filtered.fna"
         output: split=directory("{OUTDIR}/{project}/MGE/plasmid_splitted/{input_file}/")
         params: outdir="{OUTDIR}"
-        conda: "../../conda_environments/Seqkit.yml"
+        conda: "../../envs/SeqKit.yaml"
         shell: """
                 seqkit split2 -s 10000 {input} -O {wildcards.OUTDIR}/{wildcards.project}/MGE/plasmid_splitted/{wildcards.input_file}
                 """
@@ -33,7 +33,7 @@ checkpoint splitplasmid:
 rule run_PLASMID:
         input: "{OUTDIR}/{project}/MGE/plasmid_splitted/{input_file}/{file_i}.fna"
         output: temp("{OUTDIR}/{project}/MGE/plasmid/{input_file}/{file_i}_plasflow_prediction.tsv")
-        conda: "../../conda_environments/Plasmid.yml"
+        conda: "../../envs/PlasFlow.yaml"
         params: outdir="{OUTDIR}"
         shell: """
                 {config[Plasflow]} --input {input} --output {output} --threshold 0.7

rules/Toxin/Combine_Toxin_SignalP

@@ -23,7 +23,7 @@ rule R_script:
         gene_toxic=temp("{OUTDIR}/{project}/TOXIN/R_output/{input_file}_gene_table_Toxic.csv")
     message: "Run external R script to join SignalP and ToxinHMM"
     params: outdir="{OUTDIR}"
-    conda: "../../conda_environments/renv.yaml"
+    conda: "../../envs/R.yaml"
     script: "ownHMM_library.R"
 
 #Put the different files in the correct configuration

rules/Universal/Combine_PathoFact

@@ -13,7 +13,7 @@ rule combine_PathoFact:
 		Toxins="{OUTDIR}/{project}/Toxin_prediction_{input_file}_report.csv",
 		AMR_MGE="{OUTDIR}/{project}/AMR_MGE_prediction_{input_file}_report.tsv"
 	output: "{OUTDIR}/{project}/PathoFact_{input_file}_predictions.csv"
-	conda: "../../conda_environments/renv.yaml"
+	conda: "../../envs/R.yaml"
 	script: "PathoFact.R"
 
 

rules/Universal/Preprocessing

@@ -45,7 +45,7 @@ checkpoint splitting:
        output:
                splits=directory("{OUTDIR}/{project}/splitted/{input_file}/")
        params: outdir="{OUTDIR}"
-       conda: "../../conda_environments/Seqkit.yml"
+       conda: "../../envs/SeqKit.yaml"
        shell: """ 
 		seqkit split2 -s 10000 {input} -O {wildcards.OUTDIR}/{wildcards.project}/splitted/{wildcards.input_file}
 		"""	

rules/Virulence/Virulence

@@ -55,7 +55,7 @@ rule HMM_R_VIR:
                 shared="databases/models_and_domains/shared_domains.tsv",
                 ID="{OUTDIR}/{project}/renamed/{input_file}_translation.tsv"
         output: "{OUTDIR}/{project}/VIRULENCE/HMM_virulence/{input_file}.hmm_results.csv"
-        conda: "../../conda_environments/renv.yaml"
+        conda: "../../envs/R.yaml"
         script: "hmm.R"
 
 
@@ -103,31 +103,31 @@ rule HMM_VIR_finalformat:
 rule AAC:
 	input: "{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
 	output: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_AAC.txt"
-	conda: "../../conda_environments/biopython_env.yaml"
+	conda: "../../envs/Biopython.yaml"
 	shell: "python scripts/AAC.py --file {input} --out {output}"
 
 rule DPC:
         input: "{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
         output: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_DPC.txt"
-        conda: "../../conda_environments/biopython_env.yaml"
+        conda: "../../envs/Biopython.yaml"
         shell: "python scripts/DPC.py --file {input} --out {output}"
 
 rule CTDC:
         input: "{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
         output: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_CTDC.txt"
-        conda: "../../conda_environments/biopython_env.yaml"
+        conda: "../../envs/Biopython.yaml"
         shell: "python scripts/CTDC.py --file {input} --out {output}"
 
 rule CTDT:
         input: "{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
         output: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_CTDT.txt"
-        conda: "../../conda_environments/biopython_env.yaml"
+        conda: "../../envs/Biopython.yaml"
         shell: "python scripts/CTDT.py --file {input} --out {output}"
 
 rule CTDD:
         input: "{OUTDIR}/{project}/splitted/{input_file}/{file_i}.faa"
         output: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_CTDD.txt"
-        conda: "../../conda_environments/biopython_env.yaml"
+        conda: "../../envs/Biopython.yaml"
         shell: "python scripts/CTDD.py --file {input} --out {output}"
 
 rule join_matrix:
@@ -161,7 +161,7 @@ rule join_matrix:
 rule classifier:
 	input: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_matrix.tsv"
 	output: "{OUTDIR}/{project}/VIRULENCE/classifier_virulence/{input_file}/{file_i}_classifier_prediction.tsv"
-	conda: "../../conda_environments/biopython_env.yaml"
+	conda: "../../envs/Biopython.yaml"
 	shell: "python scripts/virulence_prediction.py {input} {output}"
 
 def aggregate_classifier(wildcards):