BIOWDL-310: Update TranscriptClean container to version 1.0.8

update samtools and htseq-count tasks for supporting more memory efficient counting (e.g. using name sorted bams)

Removed "pipefail" from command sections TALON and TranscriptClean

Removed "pipefail" from command sections TALON and TranscriptClean because no pipes are used. (Based on minimap2.wdl pull request)

BIOWDL-258: Add WDL task for Minimap2

 BIOWDL-260: Add WDL task for TALON

BIOWDL-259:  Add WDL task for TranscriptClean 

Combined outputDirPath and outputPrefix to outputPrefix and changed optional inputs with a default value to non optional

Update fastqsplitter