added docstring and index_bam rule, also added -e to the stringtie command

scripts/mapping

@@ -3,7 +3,7 @@ Author: Maureen Molemaker, studentnumber
 Author: Liset Eendebak, studentnumber 1014355
 script to map the fastq reads onto the reference genome
 and to annotate the transcripts
-Usage: snakemake -s mapping -c 1 # use 1 core  
+Usage: snakemake -s mapping -c <no. of cores> 
 """
 
 SAMPLES = ["20180613.A-13R1", "20180613.A-13R2", "20180613.A-13R3", 
@@ -42,6 +42,14 @@ rule sort_sam: # works for both bowtie2 and hisat2
 	shell:
 		"samtools sort -o {output} {input}"
 
+#This rule was used for validating the mapping in IGV
+#rule index_bam: # works for both bowtie2 and hisat2
+#	input:
+#		"{sample}_hisat2.bam"
+#	output:
+#		"{sample}_hisat2.bam.bai"
+#	shell:
+#		"samtools index {input}"
 
 rule gene_annotation:
 	input: 
@@ -52,7 +60,7 @@ rule gene_annotation:
 	params:
 		label="{sample}"
 	shell:
-		"stringtie -G {input.annotation} -o {output} -l {params.label} {input.bamfile}" 
+		"stringtie -G {input.annotation} -e -o {output} -l {params.label} {input.bamfile}"