Sam Nicholls
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94823e73d1
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Use xlarge-highio
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2026-06-09 12:08:19 +00:00 |
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Sam Nicholls
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fbb1529816
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Use smoke_de as default CI test
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2026-06-09 12:04:53 +00:00 |
|
Sam Nicholls
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c21588761b
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wf-transcriptomes v2.0.0
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2026-06-09 11:58:17 +00:00 |
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Sarah Griffiths
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ef08219e11
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Avoid publishing demo for transcriptomes
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2026-05-27 14:37:53 +00:00 |
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Natalia Garcia
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0ae50f9a35
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Check is a valid sample sheet use the extensive validation [CW-7210]
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2026-05-27 08:10:04 +00:00 |
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Sam Nicholls
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b6f9efd9ae
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Restore modkit test with smaller gtf, fix join error
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2026-05-26 20:12:45 +00:00 |
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Rory Munro
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1192f09bc7
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Remove bigwig CI test
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2026-05-26 16:43:05 +00:00 |
|
Sam Nicholls
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175e6c9437
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Per-sample pileup counts [CW-7196]
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2026-05-26 09:52:38 +00:00 |
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Sam Nicholls
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6c0a59581f
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CI : Exclude downloaded data artifacts
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2026-05-26 08:04:59 +00:00 |
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Kiah McIntosh
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1f456da61d
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SQANTI3 results in report [CW-7238]
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2026-05-22 15:28:21 +00:00 |
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Rory Munro
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bfebfaa4b3
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Override singularity CI
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2026-05-22 10:15:55 +00:00 |
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Sarah Griffiths
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dac0a6ef01
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Merge branch 'CW-7261-b' into 'dev'
Annotation quant issues test [CW-7261]
Closes CW-7261
See merge request epi2melabs/workflows/wf-transcriptomes!284
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2026-05-22 09:38:34 +00:00 |
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Sarah Griffiths
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7b94eb2ca0
|
Annotation quant issues test [CW-7261]
|
2026-05-22 09:38:33 +00:00 |
|
Kiah McIntosh
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f5e5f3a790
|
Alignment outputs in per sample folder [CW-7270]
|
2026-05-22 09:12:26 +00:00 |
|
Kiah McIntosh
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759cb9d868
|
Skip cohort processes when n=1 [CW-7208]
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2026-05-21 16:19:18 +00:00 |
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Natalia Garcia
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779388f871
|
Pin wf-template@ruo-next
|
2026-05-19 14:03:13 +00:00 |
|
Chris Wright
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8f093ed675
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[CW-7221] Fix various pathological cases
|
2026-05-18 10:58:18 +00:00 |
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Chris Wright
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3d7d49795e
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[CW-7235] cast ? to . in gffs
|
2026-05-16 13:22:47 +00:00 |
|
Chris Wright
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d4c9101e27
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[CW-7231] clean up ci test matrix
|
2026-05-14 21:40:48 +00:00 |
|
Chris Wright
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5af948dabf
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[CW-7214] Tidy up CLI parsing
|
2026-05-14 17:41:21 +00:00 |
|
Sam Nicholls
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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 |
|
Chris Wright
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3e0dfd21e2
|
[CW-7166] [CW-7169] Reference and annotation preparation
|
2026-05-07 10:09:36 +00:00 |
|
Chris Wright
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f180b9e331
|
[CW-7161] Add workflow-local R test infrastructure
|
2026-05-05 17:10:10 +00:00 |
|
Chris Wright
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43cf5bf42a
|
Refresh workflow to use bambu, sqanti, and dexseq
|
2026-05-05 14:10:04 +00:00 |
|
Chris Wright
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abbd3537ec
|
Bring up to date
|
2026-04-17 12:29:57 +00:00 |
|
Sarah Griffiths
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85b767358c
|
Filter out unstranded annotations and log warning [CW-6125]
|
2025-06-20 08:43:15 +00:00 |
|
Sarah Griffiths
|
11c9221edc
|
memory ci config
|
2025-04-15 11:20:42 +00:00 |
|
Sarah Griffiths
|
f9bd2ab574
|
Error message if ref_genome and ref_annotation mismatch CW-2965
|
2025-03-14 19:06:47 +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
|
c8c5922965
|
Access to undefined channel output bug CW-5398
|
2024-12-13 11:51:04 +00:00 |
|
Neil Horner
|
0a5c39cdf4
|
Account for stringtie multigene transcript artefacts
|
2024-12-12 14:30:31 +00:00 |
|
Sarah Griffiths
|
14fe76dabc
|
CW-4613 IGV config
|
2024-09-06 09:27:56 +00:00 |
|
Neil Horner
|
0200514536
|
Remove fusion detection [CW-4552]
|
2024-08-06 20:20:19 +00:00 |
|
Sarah Griffiths
|
57c0f5b303
|
Handle annotations with no strand CW-3998
|
2024-06-25 13:08:32 +00:00 |
|
Neil Horner
|
cfa41f16d0
|
BAM input CW-3512
|
2024-06-04 09:25:31 +00:00 |
|
Sarah Griffiths
|
595aae4006
|
Template update
|
2024-04-03 09:47:29 +00:00 |
|
Sarah Griffiths
|
e30d3aec98
|
DE_analysis params change input types to numeric
|
2024-02-16 10:23:15 +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
|
bf136640ed
|
No ref annotation workflow still completes
|
2024-02-07 22:50:04 +00:00 |
|
Sarah Griffiths
|
35dc9dd722
|
pychopper parameters clear up
|
2023-12-04 21:12:57 +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
|
edf3a24315
|
deal with transcriptome fasta headers that contains |
|
2023-09-06 20:18:40 +00:00 |
|
Sarah Griffiths
|
d535778497
|
add titles
|
2023-08-08 11:18:15 +00:00 |
|
Neil Horner
|
285e7c8ecf
|
Remove unused parameter
|
2023-07-26 21:09:29 +00:00 |
|
Sarah Griffiths
|
ec3c346fd8
|
fix and test for files with no gene id in attributes
|
2023-07-26 18:14:00 +00:00 |
|
Sarah Griffiths
|
df6c9a2a31
|
CW-2313 remove condition sheet requirement
|
2023-07-10 16:45:32 +00:00 |
|
Sam Nicholls
|
542f822ca6
|
Reconcile template
|
2023-07-04 10:13:05 +00:00 |
|