Based on minimap2 recommendations, the -k tag should be set to 14 for aligning directRNA Nanopore data

Add bwakit task

BIOWDL-308: Add the option for --MD tag to minimap2

BIOWDL-261: Update average memory needs for main TALON process

Co-Authored-By: DavyCats <davycats.dc@gmail.com>

Add "SampleConfigToSampleReadgroupLists" task to common.wdl

Clean up

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)