forked from wtsi-npg/p4
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Changes
134 lines (111 loc) · 6.75 KB
/
Changes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
CHANGES LOG
-----------
release 0.18.6
- Y-split fixes
When processing VTFILE nodes, make sure that parameters are reevaluated locally instead of naively inheriting values
from the enclosing template (otherwise local changes in values of components of a parameter value may be ignored).
use bambi for split by chromosome (remove java)
10-vtfp-vtfile.t - add tests for VTFILE functionality
release 0.18.5
- Correct logic in vftp.pl for allowing edges without id attributes
- Reduce verbosity in vtfp.pl
- Fix handling of splice/prune in vftp.pl where source/destination is STDIN/STOUT
- Use fopid in place of other substitutions
- use FindBin in vtfp.pl and viv.pl
release 0.18.4
- removal of -n 1 flag with seqchksum_merge.pl command in merge_aligned template to maintain current behaviour
- logging changes
correct unneeded warnings about changing use_STDIN/use_STDOUT values for INFILE/OUTFILE/RAFILE node
recognise JSON::PP:Boolean type (remove warning from log)
allow edges to have no id values (warnings about undefined values in log files should no longer appear)
- cope with differing line return behaviour of versions of rev utility (test fix)
release 0.18.3
- bwa mem flags default changes and additions
don't use -T by default
[new flag] use -K 100000000 (reads per thread, large value to make alignment runs replicable)
[new flag] use -Y to soft clip supplementary alignments instead of hard clipping
- add ability to splice and prune nodes from the final graph
- final_output_prep changes to support optional targeted stats files.
- use threaded bamsormadup in place of bamsort for coord sort
- add parameters to allow selection of java or bambi (default) implementations of i2b and decode
release 0.18.2
- propagate any 'AH' fields provided by the aligner when providing full SQ headers (bwa0.7.15)
- fix bamindexdecoder.json template: add pack option to bamindexdecoder_java_cmd array to handle undefined parameters; change default implementation from "samtools decode" to java BamIndexDecoder
release 0.18.1
- corrected typo (add_item instead of additem) which can cause compilation failure
release 0.18.0
- stage1 analysis : update to bcl_phix_deplex_wtsi_stage1_template; addition of new subgraphs
- added bcftools_genotype_call template for library merge gtcheck qc test
- added facility to allow splicing in of tee(pot) nodes at node outputs at viv.pl runtime
- remove bamcheck and add bam_stats
- added in realignment_wtsi_stage2_humansplit_template which was used to split existing target files from iRODS. Now renamed to realignment_wtsi_humansplit_template.
- changes to merge_final_output_prep to remove extra stats files and allow use of reference for existing stats files
- adding in realignment_wtsi_humansplit_notargetalign_template
- updated bamindexdecoder template (stage1 analysis) to use samtools decode by default (java version still an option)
release 0.17.3
- update Build.PL and tests to have correct and full set of requirements
release 0.17.2
- turn off compression of AlignmentFilter output
- changes to merge_final_output_prep to use tears to stream data into iRODS, generate extra stats,
use ref in stats file generation and minor tidy up.
release 0.17.1
- -n 1 flag added to seqchksum_merge.pl command in merge_aligned template to allow different tags in column 1
- scramble compression
- up to 7 for final output cram files
- down to 0 for internal bam streams
- port naming conventions (IN/OUT pre- and postfixes) adopted in templates and enforced in viv.pl
- vtfp.pl
improved error reporting
refactoring to ensure more consistent/intuitive evaluation of parameter values
allow specification of "local" parameter substitution (within a specific vtnode)
added --param_vals --export_param_vals flags
subst directive attributes ifnull and required added
remove dead code, review relevance of comments, general tidying
more tests
- add tests for viv.pl
- add (secondary stage) extra split template - remove human and another genome
release 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
release 0.16.4
- add extra branch to teepot command in to stream seqchksum output downstream (instead of using a file as an internal node)
release 0.16.3
- add tee after seqchksum (bam) output to split output to file and cmp node, to remove deadlock
- remove -s flag from all cmp commands (improve diagnostics)
- decrease teepot timeout for bmd_multiway node back to 300
release 0.16.2
- remove superfluous "-" argumant to bamseqchksum command
- increase teepot timeout for bmd_multiway node to 50000 (from 500)
release 0.16.1
- add tempdir parameter and verbose (-v) flag for teepot
release 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
release 0.15
- fix construction of alternate hash command to construct sha512primesums512 seqchksum file
release 0.14
- correct prefix value given to calibration_pu -p flag (used in output file naming - it contained an unwanted ".bam")
release 0.13
- create cram index files
release 0.12
-viv.pl
read/write to/from stdin/stdout
exec failure of a node's command is now fatal (bug fix)
-vtfp.pl
updated to use new subst_params format in templates
multiple -keys/-values pairs on the command-line now produce an array on substitution into the template
when substition of nested parameters is done, array elements which are themselves arrays are flattened
(its elements are spliced into the position of the original array); net result is that top-level
parameter substitutions result in either strings or arrays of strings
-templates
new subst_params format for production templates
changes to final_output_prep template to add flexibility to this phase of analysis (e.g. y chrom. split)
output of seqchksum files for hash type sha512primesums512 added
release 0.09
-install action should not remove lib directory at target