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[TheiaProk] Update default versions for TB-Profiler and tbp-parser #673

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merged 44 commits into from
Dec 13, 2024
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c363edb
new branch so tbp-parser is compatible
sage-wright May 3, 2024
6ea5ee8
use tbprofiler 6.2.0
sage-wright May 3, 2024
4f2165f
update tbp-parser accordingly
sage-wright May 3, 2024
947d095
int -> float
sage-wright May 3, 2024
a090f5d
change to float again and update version so it says whov2
sage-wright May 4, 2024
702185f
change to float
sage-wright May 4, 2024
4145854
remove typos ahh bad keyboard!
sage-wright May 6, 2024
2e861f4
clean up clean up everybody everywhere
sage-wright May 6, 2024
811fcc9
enable californiaDPH tbprofiler database
sage-wright May 7, 2024
763606b
enable ability to alter tbprofiler docker
sage-wright May 29, 2024
3fbe354
update docker
sage-wright Jul 5, 2024
f1c75cf
update to latest docker
sage-wright Jul 5, 2024
6e505a1
add cycloserine parameter
sage-wright Jul 5, 2024
9e4cbc8
additional params
sage-wright Sep 17, 2024
072dc98
expose input var
sage-wright Sep 26, 2024
b8b0e7d
update tbprofiler & tbp-parser defaults
sage-wright Nov 8, 2024
e0631e8
Merge branch 'main' into smw-tbprofiler-updates-dev
sage-wright Nov 8, 2024
3ccb503
add updates
sage-wright Nov 8, 2024
604ecad
update version
sage-wright Nov 8, 2024
bc9dc69
organize
sage-wright Nov 8, 2024
ab6334a
update md5sums
sage-wright Nov 12, 2024
f996a96
Merge branch 'main' into smw-tbprofiler-updates-dev
sage-wright Nov 12, 2024
e4cc386
more md5sums so sad
sage-wright Nov 12, 2024
fa19395
fix genome_percent_coverage
sage-wright Nov 12, 2024
78d24fe
rename tbprofiler_additional_outputs to call_tbp_parser
sage-wright Nov 12, 2024
749362a
clarify output
sage-wright Nov 12, 2024
563f6d2
md5sum
sage-wright Nov 12, 2024
b8d7d96
reorder trimmomatic base crop stuff
sage-wright Nov 18, 2024
ad0b3d9
add lane concatenation to theiaproks
sage-wright Nov 18, 2024
0713cdd
rewrite so it works
sage-wright Nov 19, 2024
36ff472
update documentation for concatenate_lanes
sage-wright Nov 19, 2024
eae459a
bump version and update docs
sage-wright Nov 21, 2024
682e722
update last known changes
sage-wright Nov 21, 2024
35779a6
fix md5sums
sage-wright Nov 22, 2024
92eb348
version
sage-wright Nov 25, 2024
ef96f07
update doc dockers
sage-wright Nov 25, 2024
725cd59
bump version
sage-wright Dec 11, 2024
13ad6a7
Merge branch 'main' into smw-tbprofiler-updates-dev
sage-wright Dec 11, 2024
363c10e
alphabetize things and fix description
sage-wright Dec 11, 2024
46d1005
move to appropriate type
sage-wright Dec 11, 2024
f50f62c
fix disk type
sage-wright Dec 11, 2024
5bc14bd
remove files from test
sage-wright Dec 11, 2024
04414e2
finish updating versions everywhere
sage-wright Dec 12, 2024
75c2594
add sample-level to fetch_srr_accession thing
sage-wright Dec 12, 2024
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update tbp-parser accordingly
  • Loading branch information
sage-wright committed May 3, 2024
commit 4f2165fdeef8d79b8170a1f7180910a161318539
2 changes: 1 addition & 1 deletion tasks/species_typing/mycobacterium/task_tbp_parser.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ task tbp_parser {
Float? etha237_frequency # default 0.1
File? expert_rule_regions_bed

String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.4.4"
String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.5.0"
Int disk_size = 100
Int memory = 4
Int cpu = 1
Expand Down