Sam Nicholls
|
4bc3cf727f
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Per-sample mod summary
|
2026-05-27 08:11:02 +00:00 |
|
Sam Nicholls
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74cbe196b2
|
Merge branch 'fix-ci-test-2' into 'dev'
Restore modkit test with smaller gtf, fix join error
See merge request epi2melabs/workflows/wf-transcriptomes!305
|
2026-05-26 20:12:45 +00:00 |
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Sam Nicholls
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b6f9efd9ae
|
Restore modkit test with smaller gtf, fix join error
|
2026-05-26 20:12:45 +00:00 |
|
Sam Nicholls
|
efbe4d007c
|
Shorten workflow names for log
|
2026-05-26 20:12:38 +00:00 |
|
Sam Nicholls
|
175e6c9437
|
Per-sample pileup counts [CW-7196]
|
2026-05-26 09:52:38 +00:00 |
|
Kiah McIntosh
|
1f456da61d
|
SQANTI3 results in report [CW-7238]
|
2026-05-22 15:28:21 +00:00 |
|
Neil Horner
|
d9c9cc6765
|
Add gene name to TSV outputs [CW-7160]
|
2026-05-22 10:23:21 +00:00 |
|
Kiah McIntosh
|
759cb9d868
|
Skip cohort processes when n=1 [CW-7208]
|
2026-05-21 16:19:18 +00:00 |
|
Kiah McIntosh
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d124d8ba73
|
Sort joint bambu inputs to fix caching [CW-7264]
|
2026-05-20 16:31:24 +00:00 |
|
Natalia Garcia
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dc0ebf3a52
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Simplify reference handling through the workflow prepareAnnotation [CW-7232]
|
2026-05-20 12:49:08 +00:00 |
|
Sam Nicholls
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db744dbe81
|
Scatter-gather bambu quant [CW-7201]
|
2026-05-18 12:29:48 +00:00 |
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Chris Wright
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c21c609017
|
Return the correct annotation
|
2026-05-16 17:02:03 +01:00 |
|
Chris Wright
|
5af948dabf
|
[CW-7214] Tidy up CLI parsing
|
2026-05-14 17:41:21 +00:00 |
|
Sam Nicholls
|
678f1de3f1
|
Use value channels for refs crossing samples
|
2026-05-14 17:18:57 +00:00 |
|
Sam Nicholls
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06d77b2543
|
Use new alignment ingress [CW-7186][CW-7202][CW-7229]
|
2026-05-14 09:12:38 +00:00 |
|
Kiah McIntosh
|
c783fdf6c6
|
Increase prepareAnnotationReference memory [CW-7185]
|
2026-05-08 21:04:12 +00:00 |
|
Chris Wright
|
3e0dfd21e2
|
[CW-7166] [CW-7169] Reference and annotation preparation
|
2026-05-07 10:09:36 +00:00 |
|
Chris Wright
|
63d9d14f17
|
Fix DE validation gating and per-sample NDR
|
2026-05-05 18:42:18 +01:00 |
|
Chris Wright
|
f180b9e331
|
[CW-7161] Add workflow-local R test infrastructure
|
2026-05-05 17:10:10 +00:00 |
|
Chris Wright
|
43cf5bf42a
|
Refresh workflow to use bambu, sqanti, and dexseq
|
2026-05-05 14:10:04 +00:00 |
|
Chris Wright
|
abbd3537ec
|
Bring up to date
|
2026-04-17 12:29:57 +00:00 |
|
Neil Horner
|
4fe583d4ea
|
Fix and simplify column name checking
|
2025-08-01 09:14:20 +00:00 |
|
Sarah Griffiths
|
62e4266040
|
Output dexseq file [CW-6285]
|
2025-07-29 08:54:20 +00:00 |
|
Neil Horner
|
19b54ba2ff
|
Fix hyphens in sample alias CW-5484
|
2025-05-14 13:55:01 +00:00 |
|
Sarah Griffiths
|
390739cf8a
|
Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911]
|
2025-04-03 12:57:58 +00:00 |
|
Sarah Griffiths
|
c1f784ad04
|
fix memory issue by replacing seq alignment stats with flagstat [CW-5858]
|
2025-03-31 09:20:35 +00:00 |
|
Sarah Griffiths
|
d5de051fd4
|
Only use exons in DE analysis [CW-5786]
|
2025-03-28 09:58:05 +00:00 |
|
Kiah McIntosh
|
eab8ef1efe
|
Use args for R script inputs [CW-3398]
|
2025-02-07 08:42:49 +00:00 |
|
Neil Horner
|
937a41f2cc
|
Update memory for split_bam and build_minimap_index_transcriptome
|
2025-01-03 17:06:38 +00:00 |
|
Neil Horner
|
0a5c39cdf4
|
Account for stringtie multigene transcript artefacts
|
2024-12-12 14:30:31 +00:00 |
|
Sarah Griffiths
|
465d060933
|
Actually output the dexseq file
|
2024-11-05 11:51:40 +00:00 |
|
Neil Horner
|
5c4780a1b2
|
Update report CW-3077
|
2024-10-25 15:18:05 +00:00 |
|
Sarah Griffiths
|
d83807f38d
|
Tidy de analysis
|
2024-09-16 09:26:12 +00:00 |
|
Sarah Griffiths
|
be1d322287
|
IGV absolute paths fix
|
2024-09-13 11:48:16 +00:00 |
|
Sam Nicholls
|
46363987aa
|
Output dtu_plots to local work dir then mv [CW-4886]
|
2024-09-09 18:41:17 +00:00 |
|
Neil Horner
|
0200514536
|
Remove fusion detection [CW-4552]
|
2024-08-06 20:20:19 +00:00 |
|
Sarah Griffiths
|
595aae4006
|
Template update
|
2024-04-03 09:47:29 +00:00 |
|
Sarah Griffiths
|
6a14a1d85b
|
Remove need to retry based on GTF/GFF
|
2024-02-22 09:34:38 +00:00 |
|
Sarah Griffiths
|
e3b1967872
|
Improve ref annotation transcript id version handling
|
2024-02-19 10:29:04 +00:00 |
|
Neil Horner
|
bb9acf55be
|
Resolve CW-3468 "Incorrect ids"
|
2024-02-13 08:48:21 +00:00 |
|
Neil Horner
|
d5b0cc6203
|
JAFFAL resources
|
2024-02-12 15:25:19 +00:00 |
|
Sarah Griffiths
|
4bb02049ec
|
Resource updates
|
2024-02-12 10:20:02 +00:00 |
|
Sarah Griffiths
|
1c67e3274e
|
Seperate DE files required for the report and to be output to the user
|
2024-02-09 21:45:22 +00:00 |
|
Sarah Griffiths
|
1be77ba77f
|
CW-3075 improve counts output files
|
2024-02-02 10:38:50 +00:00 |
|
Neil Horner
|
f111755d12
|
Resolve CW-3327 "Mapping 1 thread"
|
2024-01-18 19:40:14 +00:00 |
|
Neil Horner
|
d01162025a
|
Resolve CW-2369
|
2023-12-05 18:42:47 +00:00 |
|
Sarah Griffiths
|
045a077fe1
|
docs update
|
2023-12-01 12:36:33 +00:00 |
|
Sarah Griffiths
|
f683d44411
|
CW-2769 remove denovo
|
2023-09-27 08:02:00 +00:00 |
|
Sarah Griffiths
|
ab850ac67f
|
tidy up DE outputs
|
2023-08-10 10:05:11 +00:00 |
|
Sarah Griffiths
|
d535778497
|
add titles
|
2023-08-08 11:18:15 +00:00 |
|