added rules for ALFA

envs/env_alfa.yaml

+name: alfa
+channels:
+  - biocomp
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - alfa=1.1.1

snakemake/Snakefile

@@ -130,3 +130,87 @@ rule create_index_kallisto:
 		chmod -R 777 {params.output_dir}; \
 		kallisto index -i {output.index} {input.transcriptome}) &> {log}"
 
+rule generate_alfa_index:
+	''' Generate ALFA index files from sorted GTF file '''
+	input:
+		gtf = "/Users/dominikburri/Server_worker/polyasite/datasets/ref_transcriptome/refdata-cellranger-GRCh38-3.0.0/genes/genes.sorted.gtf"
+	output:
+		index_stranded = "alfa_index/sorted_genes.stranded.ALFA_index",
+		index_unstranded = "alfa_index/sorted_genes.unstranded.ALFA_index"
+	params:
+		chr_len = "CHR_LENGTH_FILE",
+		genome_index = "sorted_genes",
+		out_dir = directory("alfa_index/")
+	threads:
+		1
+	conda: 
+		"../envs/env_alfa.yaml"
+	log: 
+		"generate_alfa_index.log"
+	shell:
+		"alfa -a {input.gtf} \
+			-g {params.genome_index} \
+			-p {threads} \
+			-o {params.out_dir} &> {log}"
+
+rule star_rpm:
+	''' Create bedgraph coverage with STARs RPM normalisation '''
+	input: 
+        "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
+	output:
+		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+	params:
+		out_dir = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/",
+		filenameprefix = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_"
+	singularity:
+		"docker://zavolab/star:2.6.0a"
+	threads: 4
+	log: "logs/star_rpm.log"
+	shell:
+		"""
+		(mkdir -p {params.out_dir}; \
+		chmod -R 777 {params.out_dir}; \
+		STAR \
+		--runMode inputAlignmentsFromBAM \
+		--runThreadN {threads} \
+		--inputBAMfile {input} \
+		--outWigType "bedGraph" \
+		--outWigStrand "Stranded" \
+		--outWigNorm "RPM" \
+		--outFileNamePrefix {params.filenameprefix}) &> {log}
+		"""
+
+rule run_alfa_bg_stranded:
+	''' Run ALFA from stranded bedgraph files '''
+	input:
+		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+	output:
+		directory("output/")
+	params:
+		genome_index = "sorted_genes"
+	shell:
+		""" 
+		alfa -g {params.genome_index} \
+			-bedgraph {input} \
+			-s forward; \
+		alfa -g {params.genome_index} \
+			-bedgraph {input} \
+			-s reverse \
+			-o {output}
+		"""
+
+rule run_alfa_bg_unstranded:
+	''' Run ALFA from unstranded bedgraph files '''
+	input:
+		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+	output:
+	params:
+		genome_index = "sorted_genes"
+	shell:
+		""" 
+		alfa -g {params.genome_index} \
+			-bedgraph {input} \
+		"""
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