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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Neil Horner
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4fe583d4ea
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Fix and simplify column name checking
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2025-08-01 09:14:20 +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 |
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Neil Horner
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19b54ba2ff
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Fix hyphens in sample alias CW-5484
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2025-05-14 13:55:01 +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 |
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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 |
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Kiah McIntosh
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eab8ef1efe
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Use args for R script inputs [CW-3398]
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2025-02-07 08:42:49 +00:00 |
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Neil Horner
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937a41f2cc
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Update memory for split_bam and build_minimap_index_transcriptome
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2025-01-03 17:06:38 +00:00 |
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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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465d060933
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Actually output the dexseq file
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2024-11-05 11:51:40 +00:00 |
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Sarah Griffiths
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d83807f38d
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Tidy de analysis
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2024-09-16 09:26:12 +00:00 |
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Sarah Griffiths
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be1d322287
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IGV absolute paths fix
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2024-09-13 11:48:16 +00:00 |
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Sam Nicholls
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46363987aa
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Output dtu_plots to local work dir then mv [CW-4886]
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2024-09-09 18:41:17 +00:00 |
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Sarah Griffiths
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6a14a1d85b
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Remove need to retry based on GTF/GFF
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2024-02-22 09:34:38 +00:00 |
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Sarah Griffiths
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e3b1967872
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Improve ref annotation transcript id version handling
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2024-02-19 10:29:04 +00:00 |
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Sarah Griffiths
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1c67e3274e
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Seperate DE files required for the report and to be output to the user
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2024-02-09 21:45:22 +00:00 |
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Sarah Griffiths
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1be77ba77f
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CW-3075 improve counts output files
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2024-02-02 10:38:50 +00:00 |
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Sarah Griffiths
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045a077fe1
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docs update
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2023-12-01 12:36:33 +00:00 |
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Sarah Griffiths
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ab850ac67f
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tidy up DE outputs
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2023-08-10 10:05:11 +00:00 |
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Sarah Griffiths
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d535778497
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add titles
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2023-08-08 11:18:15 +00:00 |
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Sarah Griffiths
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b6159b2c26
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nf version
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2023-08-03 15:54:39 +00:00 |
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Sarah Griffiths
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ec3c346fd8
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fix and test for files with no gene id in attributes
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2023-07-26 18:14:00 +00:00 |
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Sarah Griffiths
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df6c9a2a31
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CW-2313 remove condition sheet requirement
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2023-07-10 16:45:32 +00:00 |
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Sarah Griffiths
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d0e7fc4b26
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CW-2308 remove real path use
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2023-06-28 17:37:49 +00:00 |
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Sarah Griffiths
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ab275b6440
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CW-1920-Annotation-file-types
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2023-05-31 20:48:35 +00:00 |
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Sarah Griffiths
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8053448d61
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CW-1882 CSV
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2023-04-04 11:54:35 +00:00 |
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Neil Horner
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d8d8a791af
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Glue
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2023-02-24 14:42:57 +00:00 |
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Sarah Griffiths
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5477e721a2
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CW-1170 Fix failed to plot
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2022-11-16 20:11:44 +00:00 |
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Sarah Griffiths
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0758f4ab51
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demo data de
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2022-11-08 18:07:44 +00:00 |
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Sarah Griffiths
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c6b6121491
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CW-649
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2022-08-23 19:15:46 +00:00 |
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