Releases: wtsi-npg/p4
Releases · wtsi-npg/p4
0.18.0
0.17.3
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
0.16.3
0.16.2
0.16.1
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