renaming out.bg based on orientation

snakemake/Snakefile

@@ -12,7 +12,11 @@ import pandas as pd
 
 samples_table = pd.read_csv(config["samples"], header=0, index_col=0, comment='#', engine='python', sep="\t")
 directionality = {"--fr": "fr-firststrand", "--rv": "fr-secondstrand"}
-
+rename_files = {"fr-firststrand": ("STAR_Signal.UniqueMultiple.out.plus.bg", 
+	"STAR_Signal.UniqueMultiple.out.minus.bg"),
+	"fr-secondstrand": ("STAR_Signal.UniqueMultiple.out.minus.bg", 
+	"STAR_Signal.UniqueMultiple.out.plus.bg")}
+	
 localrules: finish
 
 ##################################################################################

snakemake/paired_end.snakefile.smk

@@ -401,7 +401,6 @@ rule star_rpm_paired_end:
 		--outFileNamePrefix {params.prefix}) &> {log}
 		"""
 
-
 rule alfa_bg_paired_end:
 	''' Run ALFA from stranded bedgraph files '''
 	input:
@@ -438,14 +437,14 @@ rule alfa_bg_paired_end:
 			"paired_end",
 			"{sample}",
 			"ALFA")),
+		orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]],
 		in_file_str1 = "STAR_Signal.UniqueMultiple.str1.out.bg",
-		rename_str1 = "STAR_Signal.UniqueMultiple.out.plus.bg",
+		rename_str1 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][0],
 		in_file_str2 = "STAR_Signal.UniqueMultiple.str2.out.bg",
-		rename_str2 = "STAR_Signal.UniqueMultiple.out.minus.bg",
+		rename_str2 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][1],
 		genome_index = lambda wildcards: os.path.abspath(os.path.join(config["alfa_indexes"], samples_table.loc[wildcards.sample, "organism"], 
 			str(samples_table.loc[wildcards.sample, "index_size"]), "ALFA", "sorted_genes")),
-		name = "{sample}",
-		orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]
+		name = "{sample}"
 	singularity:
 		"docker://zavolab/alfa:1.1.1"
 	log: os.path.abspath(os.path.join(config["local_log"], "paired_end", "{sample}", "alfa_bg_paired_end.log"))

snakemake/single_end.snakefile.smk

@@ -364,14 +364,14 @@ rule alfa_bg_single_end:
 			"single_end",
 			"{sample}",
 			"ALFA")),
+		orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]],
 		in_file_str1 = "STAR_Signal.UniqueMultiple.str1.out.bg",
-		rename_str1 = "STAR_Signal.UniqueMultiple.out.plus.bg",
+		rename_str1 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][0],
 		in_file_str2 = "STAR_Signal.UniqueMultiple.str2.out.bg",
-		rename_str2 = "STAR_Signal.UniqueMultiple.out.minus.bg",
+		rename_str2 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][1],
 		genome_index = lambda wildcards: os.path.abspath(os.path.join(config["alfa_indexes"], samples_table.loc[wildcards.sample, "organism"], 
 			str(samples_table.loc[wildcards.sample, "index_size"]), "ALFA", "sorted_genes")),
-		name = "{sample}",
-		orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]
+		name = "{sample}"
 	singularity:
 		"docker://zavolab/alfa:1.1.1"
 	log: os.path.abspath(os.path.join(config["local_log"], "single_end", "{sample}", "alfa_bg_single_end.log"))