change split genomes from output to param

The `directory` directive touches an empty file within the directory.
This causes WIsH to iterate over that file and messes its output. It
contains an empty string as contig and contains an empty phage entry
with a random taxonomy assignment. By making it a parameter for the
rules the dir only contains fasta files.

workflow/Snakefile

@@ -54,26 +54,26 @@ rule split_multifasta:
 	input:
 		multifasta_fp = get_sample_fasta
 	output:
-		genomes_dir = directory("results/{sample}/tmp/genomes"),
 		reflist = "results/{sample}/tmp/reflist.txt"
 	log: "logs/{sample}/split_multifasta.log"
+	params:
+		genomes_dir = "results/{sample}/tmp/genomes",
 	shell:
-		"mkdir -p {output.genomes_dir} && "
+		"mkdir -p {params.genomes_dir} && "
 		"python workflow/scripts/split_multifasta.py "
 		"-i {input.multifasta_fp} "
-		"-o {output.genomes_dir} "
+		"-o {params.genomes_dir} "
 		"--write-reflist &>{log}"
 
 # vHULK
 rule run_vhulk:
 	input:
-		fasta_dir = rules.split_multifasta.output.genomes_dir,
 		reflist = rules.split_multifasta.output.reflist
 	output:
 		done_txt = touch("results/{sample}/vhulk/.done.txt"),
 		results_csv = "results/{sample}/vhulk/results/results.csv"
 	params:
-		input_dir = "results/{sample}/tmp/genomes",
+		fasta_dir = "results/{sample}/tmp/genomes",
 		output_dir = "results/{sample}/vhulk"
 	log: 
 		"logs/{sample}/vhulk.log"
@@ -81,9 +81,9 @@ rule run_vhulk:
 		"library://papanikos_182/default/vhulk:0.1"
 	threads: 8
 	shell:
-		"vHULK-v0.1.py -i {params.input_dir} "
+		"vHULK-v0.1.py -i {params.fasta_dir} "
 		"-t {threads} &>{log} && "
-		"mv {input.fasta_dir}/results {params.output_dir}"
+		"mv {params.fasta_dir}/results {params.output_dir}"
 
 rule filter_vhulk:
 	input:
@@ -100,19 +100,19 @@ rule run_rafah:
 	input:
 		# Run vhulk first since it writing in the input
 		rules.run_vhulk.output.done_txt,
-		fasta_dir = rules.split_multifasta.output.genomes_dir,
 		reflist = rules.split_multifasta.output.reflist,
 	output:
 		seq_info = "results/{sample}/rafah/{sample}_Seq_Info.tsv"
 	params:
-		prefix = "results/{sample}/rafah/{sample}"
+		prefix = "results/{sample}/rafah/{sample}",
+		fasta_dir = "results/{sample}/tmp/genomes"
 	log:
 		"logs/{sample}/rafah.log"
 	container: 
 		"library://papanikos_182/default/rafah:0.1"
 	threads: 8
 	shell:
-		"RaFAH_v0.1.pl --genomes_dir {input.fasta_dir}/ "
+		"RaFAH_v0.1.pl --genomes_dir {params.fasta_dir}/ "
 		"--extension fasta --threads {threads} "
 		"--file_prefix {params.prefix} "
 		"&>{log}"
@@ -130,7 +130,6 @@ rule run_vhmnet:
 	input:
 		# Run vhulk first since it writing in the input
 		rules.run_vhulk.output.done_txt,
-		fasta_dir = rules.split_multifasta.output.genomes_dir,
 		reflist = rules.split_multifasta.output.reflist,
 	output:
 		done = touch("results/{sample}/vhmnet/.done.txt")
@@ -140,18 +139,19 @@ rule run_vhmnet:
 		data_dir = "/data",
 		#data_dir = DATA_DIR,
 		tmp_dir = "results/{sample}/vhmnet/tmp",
-		output_dir = "results/{sample}/vhmnet"
+		output_dir = "results/{sample}/vhmnet",
+		fasta_dir = "results/{sample}/tmp/genomes"
 	threads: 8
 	container:
 		"library://papanikos_182/default/vhmnet:0.1"
 	log:
 		"logs/{sample}/vhmnet.log"
 	shell:
-		"VirHostMatcher-Net.py -q {input.fasta_dir} "
+		"VirHostMatcher-Net.py -q {params.fasta_dir} "
 		"-t {threads} "
 		"-i {params.tmp_dir} "
 		"-d {params.data_dir} "
-		"-q {input.fasta_dir} "
+		"-q {params.fasta_dir} "
 		"-o {params.output_dir} "
 		"&>{log}"
 
@@ -179,8 +179,7 @@ rule run_wish:
 	input:
 		# Run vhulk first since it writing in the input
 		rules.run_vhulk.output.done_txt,
-		fasta_dir = rules.split_multifasta.output.genomes_dir,
-		reflist = rules.split_multifasta.output.genomes_dir,
+		reflist = rules.split_multifasta.output.reflist,
 	output:
 		prediction_list = "results/{sample}/wish/prediction.list",
 		ll_mat = "results/{sample}/wish/llikelihood.matrix"
@@ -194,10 +193,11 @@ rule run_wish:
 		# see run_vhmnet rule
 		models_dir = "/data/host_wish_model",
 		#models_dir = DATA_DIR.joinpath("host_wish_model"),
-		output_dir = "results/{sample}/wish"
+		output_dir = "results/{sample}/wish",
+		fasta_dir = "results/{sample}/tmp/genomes"
 	shell:
 		"mkdir -p {params.output_dir} && "
-		"WIsH -c predict -g {input.fasta_dir} "
+		"WIsH -c predict -g {params.fasta_dir} "
 		"-t {threads} -b "
 		"-m {params.models_dir} -r {params.output_dir} "
 		"&>{log}"