Include sample name into the TopHat result files

TopHat, in particular, generates the following output files into a folder, specified in the "Output folder" parameter of the element:

• accepted_hits.bam
• junctions.bed
• insertions.bed
• deletions.bed

In 1.31 modify this as follows (note that this may be further improved in future): automatically rename the output files as follows:

• samplename.bam
• samplename_junctions.bed
• samplename_insertions.bed
• samplename_deletions.bed

Here "samplename" is generated automatically based on the input file names (consider scenarios when SE and PE reads are input).

Note that this issue is important for usability of the "RNA-Seq analysis with TopHat and StringTie" workflow. A report, generated by "StringTie Gene Abundance Report", uses input file names to distinguish different samples.