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 |
|
Chris Wright
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abbd3537ec
|
Bring up to date
|
2026-04-17 12:29:57 +00:00 |
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Sarah Griffiths
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62e4266040
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Output dexseq file [CW-6285]
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2025-07-29 08:54:20 +00:00 |
|
Sarah Griffiths
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85b767358c
|
Filter out unstranded annotations and log warning [CW-6125]
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2025-06-20 08:43:15 +00:00 |
|
Neil Horner
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b2ac1edbb9
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Container update CW-5998
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2025-05-16 08:38:28 +00:00 |
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Sarah Griffiths
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390739cf8a
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Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911]
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2025-04-03 12:57:58 +00:00 |
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Sarah Griffiths
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c1f784ad04
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fix memory issue by replacing seq alignment stats with flagstat [CW-5858]
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2025-03-31 09:20:35 +00:00 |
|
Sarah Griffiths
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d5de051fd4
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Only use exons in DE analysis [CW-5786]
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2025-03-28 09:58:05 +00:00 |
|
Sarah Griffiths
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f9bd2ab574
|
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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b62722751f
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Fix overwritten DGE results file
|
2025-02-18 17:05:45 +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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0ec44d03bd
|
Empty GFF bug CW-5438
|
2024-12-18 15:01:33 +00:00 |
|
Neil Horner
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c8c5922965
|
Access to undefined channel output bug CW-5398
|
2024-12-13 11:51:04 +00:00 |
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Sarah Griffiths
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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 |
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Sarah Griffiths
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d83807f38d
|
Tidy de analysis
|
2024-09-16 09:26:12 +00:00 |
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Sarah Griffiths
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be1d322287
|
IGV absolute paths fix
|
2024-09-13 11:48:16 +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 |
|
Neil Horner
|
0200514536
|
Remove fusion detection [CW-4552]
|
2024-08-06 20:20:19 +00:00 |
|
Neil Horner
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1fed562746
|
Merge branch 'pychop_threads_CW-4010' into 'dev'
Give pychopper more threads
See merge request epi2melabs/workflows/wf-transcriptomes!174
|
2024-06-25 14:11:28 +00:00 |
|
Neil Horner
|
411290d5a4
|
Give pychopper more threads
|
2024-06-25 14:11:28 +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
|
cfa41f16d0
|
BAM input CW-3512
|
2024-06-04 09:25:31 +00:00 |
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Sarah Griffiths
|
d7fcb2d5f7
|
Temp update
|
2024-05-10 08:42:12 +00:00 |
|
Neil Horner
|
bb9acf55be
|
Resolve CW-3468 "Incorrect ids"
|
2024-02-13 08:48:21 +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 |
|
Neil Horner
|
fdb938a147
|
Publish isoforms table
|
2024-02-09 10:59:01 +00:00 |
|
Sarah Griffiths
|
bf136640ed
|
No ref annotation workflow still completes
|
2024-02-07 22:50:04 +00:00 |
|
Sarah Griffiths
|
1be77ba77f
|
CW-3075 improve counts output files
|
2024-02-02 10:38:50 +00:00 |
|
Sarah Griffiths
|
3acf993586
|
de_analysis include in sample cmd
|
2023-12-08 09:32:07 +00:00 |
|
Neil Horner
|
d01162025a
|
Resolve CW-2369
|
2023-12-05 18:42:47 +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 |
|
Sam Nicholls
|
bb99170130
|
Template updates [CW-1564][CW-2303][CW-2855]
|
2023-10-16 14:17:32 +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
|
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 |
|
Sarah Griffiths
|
b6159b2c26
|
nf version
|
2023-08-03 15:54:39 +00:00 |
|
Sarah Griffiths
|
df6c9a2a31
|
CW-2313 remove condition sheet requirement
|
2023-07-10 16:45:32 +00:00 |
|
Sarah Griffiths
|
d0e7fc4b26
|
CW-2308 remove real path use
|
2023-06-28 17:37:49 +00:00 |
|
Sarah Griffiths
|
9f449ae467
|
CW-2188 add test for denovo plus warnings
|
2023-06-14 13:21:27 +00:00 |
|
Sarah Griffiths
|
ab275b6440
|
CW-1920-Annotation-file-types
|
2023-05-31 20:48:35 +00:00 |
|
Sarah Griffiths
|
8053448d61
|
CW-1882 CSV
|
2023-04-04 11:54:35 +00:00 |
|
Neil Horner
|
d8d8a791af
|
Glue
|
2023-02-24 14:42:57 +00:00 |
|
Sarah Griffiths
|
43e746f0ea
|
schema updates
|
2022-12-01 21:05:01 +00:00 |
|
Sarah Griffiths
|
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 |
|
Sarah Griffiths
|
a111cae834
|
CW-1167: error if conditionsheet and sample sheet dont match
|
2022-11-15 14:59:43 +00:00 |
|