Robust handling of sam/bam file

[hwlim]

1. Temporary files remain after run

   • There are many temporary files left over in the scratch folder including sam and tmp, which need to be cleaned up
   • If there is not clear advantage, any alignment results would better be stored in bam. It can be done simple piping e.g. hisat2-3n ###### | samtools view -b > align.bam

2. Safer temporary file names

   • Currently, the temporary files are named by simply following the sample name
   • This is not safe because the same name can be used in other datasets
   • Whenever creating temporary files, it is strongly recommended to use random name
   • Please update it. Here is an example in bash environment

>> tmp=`mktemp -p ${TMPDIR}`
>> hisat-3n ......... -S ${tmp}
>> samtools sort ${tmp} -o {output.bam}

This is just an example, sam file better be bam file

[cahn20]

Addressed in pull request #10