corrected alfa_index

Snakefile

@@ -334,22 +334,22 @@ rename_expr = {"fr-firststrand": ("out.plus", "out.minus"),
 rule generate_alfa_index:
 	''' Generate ALFA index files from sorted GTF file '''
 	input:
-		gtf =lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0]
-	output:
-		index_stranded = os.path.join(config["alfa_indexes"], "{organism}", 
-			"{index_size}", "ALFA", "sorted_genes.stranded.ALFA_index"),
-		index_unstranded = os.path.join(config["alfa_indexes"], "{organism}", 
-			"{index_size}", "ALFA", "sorted_genes.unstranded.ALFA_index")
-	params:
+		gtf = lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0],
 		chr_len = os.path.join(
 			config["star_indexes"],
 			"{organism}",
 			"{index_size}",
 			"STAR_index",
 			"chrNameLength.txt"),
+	output:
+		index_stranded = os.path.join(config["alfa_indexes"], "{organism}", 
+			"{index_size}", "ALFA", "sorted_genes.stranded.ALFA_index"),
+		index_unstranded = os.path.join(config["alfa_indexes"], "{organism}", 
+			"{index_size}", "ALFA", "sorted_genes.unstranded.ALFA_index")
+	params:
 		genome_index = "sorted_genes",
-		out_dir = directory(os.path.join(config["alfa_indexes"], "{organism}", "{index_size}", "ALFA"))
-	threads:	4
+		out_dir = lambda wildcards, output: os.path.basename(output.index_stranded)
+	threads: 4
 	singularity: 
 		"docker://zavolab/alfa:1.1.1"
 	log: 
@@ -357,7 +357,7 @@ rule generate_alfa_index:
 	shell:
 		"alfa -a {input.gtf} \
 			-g {params.genome_index} \
-			--chr_len {params.chr_len} \
+			--chr_len {input.chr_len} \
 			-p {threads} \
 			-o {params.out_dir} &> {log}"
 

scripts/labkey_to_snakemake.py

@@ -311,6 +311,7 @@ def main():
   kallisto_indexes: "results/kallisto_indexes/"
   salmon_indexes: "results/salmon_indexes/"
   star_indexes: "results/star_indexes/"
+  alfa_indexes: "results/alfa_indexes/"
 ...''')
 
     sys.stdout.write('Create snakemake table finished successfully...\n')