viv.pl - enhanced error message
vtfp.pl - added ability to link one output to several inouts in a subgraph (VTFILE node)
added refactored templates for stage 2 alignment and realignment
corrected execute bit on viv.pl
pre_alignment_realign.json - corrected "bamreset resetaux=0..." to "bamreset resetaux=1...", and "bamadapterclip" to "bamadapterfind clip=1"
added auxfilter list to bamreset in auxmerge_prep_realign.json
corrected bamadapterclip to bamadapterfind clip=1
some amendment of subst_param names in template
changed potentially problematic duplicate subst_param name: final_output_prep to final_output_prep_target_name and final_output_prep_phix_name
added bamrecompress flags to produce md5 and bam index files (as in production pipeline)
corrected default VTFILE for pre_alignment node in wtsi_realignment_stage2_template
added README for new vtlib temnplates
final_output_prep.json - corrected construction of flags for bam index and md5 files
added calibration_pu node to final_output_prep subgraph
renamed templates for consistency with current production templates
corrected mistake in template
Merge remote-tracking branch 'kl2-remote/refactored_templates' into HEAD
added "--keep-fasta-order" to tophat command (as in current production template)
Merge remote-tracking branch 'kl2-remote/refactored_templates' into HEAD