ALFA (un)stranded works for chr21.bam #18

snakemake/Snakefile

@@ -149,27 +149,31 @@ rule generate_alfa_index:
 	singularity: 
 		"docker://zavolab/alfa:1.1.1"
 	log: 
-		"generate_alfa_index.log"
+		"logs/generate_alfa_index.log"
 	shell:
 		"alfa -a {input.gtf} \
 			-g {params.genome_index} \
 			-p {threads} \
 			-o {params.out_dir} &> {log}"
 
+# TODO: test with chr21.bam
+# add singularity-args to this chr21.bam path
 rule star_rpm_stranded:
 	''' Create stranded bedgraph coverage with STARs RPM normalisation '''
 	input: 
-        "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
+		bam = "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
 	output:
-		"/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
-		"/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+		str1 = ("/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.Unique.str1.out.bg",
+			"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str1.out.bg"),
+		str2 = ("/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str2.out.bg",
+			"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str2.out.bg")
 	params:
-		out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/",
-		filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_"
+		out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/",
+		filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_"
 	singularity:
 		"docker://zavolab/star:2.6.0a"
 	threads: 4
-	log: "logs/star_rpm.log"
+	log: "logs/star_rpm_stranded.log"
 	shell:
 		"""
 		(mkdir -p {params.out_dir}; \
@@ -177,31 +181,38 @@ rule star_rpm_stranded:
 		STAR \
 		--runMode inputAlignmentsFromBAM \
 		--runThreadN {threads} \
-		--inputBAMfile {input} \
+		--inputBAMfile {input.bam} \
 		--outWigType "bedGraph" \
 		--outWigStrand "Stranded" \
 		--outWigNorm "RPM" \
 		--outFileNamePrefix {params.filenameprefix}) &> {log}
 		"""
 
+# TODO: test with chr21.bam
 rule run_alfa_bg_stranded:
 	''' Run ALFA from stranded bedgraph files '''
 	input:
-		str1 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
-		str2 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+		str1 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str1.out.bg",
+		str2 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/STAR_Signal.UniqueMultiple.str2.out.bg"
 	output:
-		directory("output/")
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/ALFA_plots.Biotypes.pdf",
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_stranded/ALFA_plots.Categories.pdf"
 	params:
-		genome_index = "sorted_genes"
+		out_dir = "alfa_stranded",
+		in_file_str1 = "STAR_Signal.UniqueMultiple.str1.out.bg",
+		in_file_str2 = "STAR_Signal.UniqueMultiple.str2.out.bg",
+		genome_index = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_index/sorted_genes",
+		name_str1 = "test_chr21_str1",
+		name_str2 = "test_chr21_str2"
+	singularity:
+		"docker://zavolab/alfa:1.1.1"
+	log: "../logs/alfa_bg_stranded.log"
 	shell:
 		""" 
+		cd {params.out_dir}; \
 		alfa -g {params.genome_index} \
-			-bedgraph {input} \
-			-s forward; \
-		alfa -g {params.genome_index} \
-			-bedgraph {input} \
-			-s reverse \
-			-o {output}
+			--bedgraph {params.in_file_str1} {params.name_str1} {params.in_file_str2} {params.name_str2} \
+			&> {log}
 		"""
 
 rule star_rpm_unstranded:
@@ -209,14 +220,15 @@ rule star_rpm_unstranded:
 	input: 
 		bam = "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
 	output:
-		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg"
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_Signal.Unique.str1.out.bg",
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_Signal.UniqueMultiple.str1.out.bg"
 	params:
-		out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/",
-		filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_"
+		out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/",
+		filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_"
 	singularity:
 		"docker://zavolab/star:2.6.0a"
 	threads: 4
-	log: "logs/star_rpm.log"
+	log: "logs/star_rpm_unstranded.log"
 	shell:
 		"""
 		(mkdir -p {params.out_dir}; \
@@ -234,12 +246,12 @@ rule star_rpm_unstranded:
 rule run_alfa_bg_unstranded:
 	''' Run ALFA from unstranded bedgraph files '''
 	input:
-		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg"
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/STAR_Signal.UniqueMultiple.str1.out.bg"
 	output:
-		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/ALFA_plots.Biotypes.pdf",
-		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/star_rpm/ALFA_plots.Categories.pdf"
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/ALFA_plots.Biotypes.pdf",
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_unstranded/ALFA_plots.Categories.pdf"
 	params:
-		out_dir = "star_rpm",
+		out_dir = "alfa_unstranded",
 		in_file = "STAR_Signal.UniqueMultiple.str1.out.bg",
 		genome_index = "/scicore/home/zavolan/burri0000/rnaseqpipeline/snakemake/alfa_index/sorted_genes",
 		name = "test_chr21"