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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Sam Nicholls
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9cba80832d
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Merge branch 'unnecessary-igv' into 'dev'
Publish refs for IGV only when necessary [CW-7280]
See merge request epi2melabs/workflows/wf-transcriptomes!306
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2026-05-27 12:24:08 +00:00 |
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Sam Nicholls
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262f49944e
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Publish refs for IGV only when necessary [CW-7280]
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2026-05-27 12:24:07 +00:00 |
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Natalia Garcia
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531975c004
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Template updates: sort threads param
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2026-05-27 11:59:11 +00:00 |
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Sam Nicholls
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dda764f48c
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Merge branch 'cw-7196-b' into 'dev'
Per-sample mod summary
See merge request epi2melabs/workflows/wf-transcriptomes!294
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2026-05-27 08:11:02 +00:00 |
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Sam Nicholls
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4bc3cf727f
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Per-sample mod summary
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2026-05-27 08:11:02 +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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74cbe196b2
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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
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2026-05-26 20:12:45 +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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Sam Nicholls
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efbe4d007c
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Shorten workflow names for log
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2026-05-26 20:12:38 +00:00 |
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Natalia Garcia
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6ca2f2f027
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Tidy up schema validation [CW-7278]
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2026-05-26 18:42:11 +00:00 |
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Sarah Griffiths
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3ca4511b5b
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Add force alignment option [CW-7274]
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2026-05-26 14:44:50 +00:00 |
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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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Natalia Garcia
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c87a5ce09c
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Merge branch 'CW-7212' into 'dev'
Exclude non existent samples or samples without reads after ingress
Closes CW-7212
See merge request epi2melabs/workflows/wf-transcriptomes!255
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2026-05-26 07:53:34 +00:00 |
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Natalia Garcia
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04ddfbf872
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Exclude non existent samples or samples without reads after ingress
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2026-05-26 07:53:34 +00:00 |
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Neil Horner
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020d555219
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Add the missing annotation ref summary [CW-7271]
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2026-05-22 17:05:56 +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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Neil Horner
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5823f04809
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[CW-7211] Hierarchical plot + PCA
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2026-05-22 14:34:50 +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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4dfd5f06e7
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Restore IGV [CW-7234]
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2026-05-18 09:41:49 +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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Natalia Garcia
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d7337638f8
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Add missing directives [CW-7191]
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2026-05-08 14:56:31 +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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9dd5895482
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Exclude ingress samples with no reads
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2026-05-05 16:40:24 +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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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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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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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 |
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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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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 |
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Neil Horner
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b62722751f
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Fix overwritten DGE results file
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2025-02-18 17:05:45 +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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0ec44d03bd
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Empty GFF bug CW-5438
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2024-12-18 15:01:33 +00:00 |
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Neil Horner
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c8c5922965
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Access to undefined channel output bug CW-5398
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2024-12-13 11:51:04 +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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Neil Horner
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5c4780a1b2
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Update report CW-3077
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2024-10-25 15:18:05 +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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Sarah Griffiths
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14fe76dabc
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CW-4613 IGV config
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2024-09-06 09:27:56 +00:00 |
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Neil Horner
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0200514536
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Remove fusion detection [CW-4552]
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2024-08-06 20:20:19 +00:00 |
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Neil Horner
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1fed562746
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Merge branch 'pychop_threads_CW-4010' into 'dev'
Give pychopper more threads
See merge request epi2melabs/workflows/wf-transcriptomes!174
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2024-06-25 14:11:28 +00:00 |
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Neil Horner
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411290d5a4
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Give pychopper more threads
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2024-06-25 14:11:28 +00:00 |
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Sarah Griffiths
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57c0f5b303
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Handle annotations with no strand CW-3998
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2024-06-25 13:08:32 +00:00 |
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Neil Horner
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cfa41f16d0
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BAM input CW-3512
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2024-06-04 09:25:31 +00:00 |
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Sarah Griffiths
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d7fcb2d5f7
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Temp update
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2024-05-10 08:42:12 +00:00 |
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Neil Horner
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bb9acf55be
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Resolve CW-3468 "Incorrect ids"
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2024-02-13 08:48:21 +00:00 |
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