Delete mapping

mapping

-#ftp.sra.ebi.ac.uk/vol1/run/ERR462/ERR4627(061)/201806(13.A-10R1)_R1.fastq.gz
-#, "20180613.A-10R2"
-SAMPLES = ["20180613.A-10R1", "20180613.A-10R2"]
-
-
-rule all:
-	input:
-		expand("{sample}_hisat2.gtf", sample=SAMPLES)
-
-#leaf 288 R4_2 has a different name
-rule mapping:
-	input:
-		reads = "../transcriptome/{sample}_R1.fastq.gz",
-		index = "../Arabidopsis_thaliana/TAIR.1.ht2",
-	output:
-		"{sample}_hisat2.sam",
-	params:
-		index="../Arabidopsis_thaliana/TAIR",
-	shell: 
-		"hisat2 -p 1 -x  {params.index} -U {input.reads} -S {output}"
-		
-rule sort_sam: # works for both bowtie2 and hisat2
-	input:
-		"{sample}_hisat2.sam"
-	output:
-		"{sample}_hisat2.bam"
-	shell:
-		"samtools sort -o {output} {input}"
-		
-rule stringtie:
-	input: 
-		bamfile = "{sample}_hisat2.bam",
-		annotation = "../Arabidopsis_thaliana/genes.gtf",
-	output:
-		"{sample}_hisat2.gtf"
-	params:
-		label="{sample}"
-	shell:
-		"stringtie -G {input.annotation} -o {output} -l {params.label} {input.bamfile}" 
-
-
-