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
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Annotation quant issues test [CW-7261]
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2026-05-22 09:38:33 +00:00 |
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Kiah McIntosh
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f5e5f3a790
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Alignment outputs in per sample folder [CW-7270]
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2026-05-22 09:12:26 +00:00 |
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Kiah McIntosh
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759cb9d868
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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
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Pin wf-template@ruo-next
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2026-05-19 14:03:13 +00:00 |
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Chris Wright
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8f093ed675
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[CW-7221] Fix various pathological cases
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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
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2026-05-16 13:22:47 +00:00 |
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Chris Wright
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d4c9101e27
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[CW-7231] clean up ci test matrix
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2026-05-14 21:40:48 +00:00 |
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Chris Wright
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5af948dabf
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[CW-7214] Tidy up CLI parsing
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2026-05-14 17:41:21 +00:00 |
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Sam Nicholls
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678f1de3f1
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Use value channels for refs crossing samples
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2026-05-14 17:18:57 +00:00 |
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Sam Nicholls
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06d77b2543
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Use new alignment ingress [CW-7186][CW-7202][CW-7229]
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2026-05-14 09:12:38 +00:00 |
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Chris Wright
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3e0dfd21e2
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[CW-7166] [CW-7169] Reference and annotation preparation
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2026-05-07 10:09:36 +00:00 |
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Chris Wright
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f180b9e331
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[CW-7161] Add workflow-local R test infrastructure
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2026-05-05 17:10:10 +00:00 |
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Chris Wright
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43cf5bf42a
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Refresh workflow to use bambu, sqanti, and dexseq
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2026-05-05 14:10:04 +00:00 |
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Chris Wright
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abbd3537ec
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Bring up to date
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2026-04-17 12:29:57 +00:00 |
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Sarah Griffiths
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85b767358c
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Filter out unstranded annotations and log warning [CW-6125]
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2025-06-20 08:43:15 +00:00 |
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Sarah Griffiths
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11c9221edc
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memory ci config
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2025-04-15 11:20:42 +00:00 |
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Sarah Griffiths
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f9bd2ab574
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Error message if ref_genome and ref_annotation mismatch CW-2965
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2025-03-14 19:06:47 +00:00 |
|
Neil Horner
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937a41f2cc
|
Update memory for split_bam and build_minimap_index_transcriptome
|
2025-01-03 17:06:38 +00:00 |
|
Neil Horner
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c8c5922965
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Access to undefined channel output bug CW-5398
|
2024-12-13 11:51:04 +00:00 |
|
Neil Horner
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0a5c39cdf4
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Account for stringtie multigene transcript artefacts
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2024-12-12 14:30:31 +00:00 |
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Sarah Griffiths
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14fe76dabc
|
CW-4613 IGV config
|
2024-09-06 09:27:56 +00:00 |
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Neil Horner
|
0200514536
|
Remove fusion detection [CW-4552]
|
2024-08-06 20:20:19 +00:00 |
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Sarah Griffiths
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57c0f5b303
|
Handle annotations with no strand CW-3998
|
2024-06-25 13:08:32 +00:00 |
|
Neil Horner
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cfa41f16d0
|
BAM input CW-3512
|
2024-06-04 09:25:31 +00:00 |
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Sarah Griffiths
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595aae4006
|
Template update
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2024-04-03 09:47:29 +00:00 |
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Sarah Griffiths
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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 |
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Sarah Griffiths
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ec3c346fd8
|
fix and test for files with no gene id in attributes
|
2023-07-26 18:14:00 +00:00 |
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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 |
|
Sarah Griffiths
|
9f449ae467
|
CW-2188 add test for denovo plus warnings
|
2023-06-14 13:21:27 +00:00 |
|
Sarah Griffiths
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ab275b6440
|
CW-1920-Annotation-file-types
|
2023-05-31 20:48:35 +00:00 |
|
Sarah Griffiths
|
1d5fcdd211
|
transcriptomes mac ci arm 64
|
2023-05-16 20:54:23 +00:00 |
|
Sarah Griffiths
|
43e746f0ea
|
schema updates
|
2022-12-01 21:05:01 +00:00 |
|
Sarah Griffiths
|
5de212cf57
|
Move data to AWS
|
2022-11-16 18:49:53 +00:00 |
|
Sarah Griffiths
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cd1f97de4e
|
CW-1162 option to run DE without assembly transcriptome
|
2022-11-16 12:16:38 +00:00 |
|
Neil Horner
|
e339446a8a
|
Fix for when JAFFAL returns exit status 1 when no fusions are found
|
2022-11-15 19:56:46 +00:00 |
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Sarah Griffiths
|
0758f4ab51
|
demo data de
|
2022-11-08 18:07:44 +00:00 |
|
Sarah Griffiths
|
c6b6121491
|
CW-649
|
2022-08-23 19:15:46 +00:00 |
|
Neil Horner
|
956c80573a
|
Fusions
|
2022-08-01 12:01:01 +00:00 |
|