0.18.0

stage1 analysis
splicing in of tee nodes at node outputs (viv.pl)
remove bamcheck and add bam_stats
updates to realignment and merge templates

0.17.3

patch release to correct and update build dependencies (Build.PL and test files)

0.17.2

release 0.17.2

0.17.1

vtfp.pl
added '-param_vals' and '--export_param_vals' flags
subst directive attributes "ifnull" and "required" added
allow specification of local parameter substitution (within a specific vtnode)
improved error reporting

viv.pl: in/output port naming convention (*IN_, _OUT, IN, or *OUT__) for nodes and edges now mandatory

templates
secondary stage extra split template added - remove human and another genome
scramble compression up to 7 for final output cram files; down to 0 for internal bam streams

0.17

• human split with no target align (secondary stage) template introduced
• initial work for stage one (bcl, adapter, phiX and spatial filter to split processing) using templates
• bammarkduplicates reintroduced for unaligned file because downstream qc processing relies on presence of markdups_metrics file
• library cram merging: merge_aligned.json and merge_final_output_prep.json
• remove potential deadlock by using non-blocking open of STDIN

0.16.4

add extra branch to teepot command in to stream seqchksum output downstream (instead of using a file as an internal node)

0.16.3

add new tee for seqchksum in bam/cram comparison in final_output_pre template to avoid deadlock
revert timeout to 300 for bmd_multiway teepot command to avoid processing delays
remove -s from cmp commands for increased diagnostics for failure

0.16.2

remove unneeded argument from bamseqchksum
inclrease teepot timeout to 30000 (from 300) for bmd_multiway node in final_output_prep template

0.16.1

addition of -v (verbose) and -t (tempdir location) flags to teepot commands in templates

0.16

• human split: new alignment_wtsi_stage2_humansplit_template.json, seqchksum_hs.json; addition of subst_params to alignment_common
• seqchksum comparisons: merge bamseqchksum files for outputs for comparison with initial bam file in seqchksum.json
• added comparison of cram and bam seqchksum within final_output_prep
• scramble reference optional in final_output_prep template (reference name passed as a parameter instead of via subgraph_io)
• realignment templates fixes/amendents: default value for common subst_params file; default to cram input