kfukuta/wf-transcriptomes-v202
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62e4266040
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Author SHA1 Message Date
Sarah Griffiths
62e4266040 Output dexseq file [CW-6285] 2025-07-29 08:54:20 +00:00
Sarah Griffiths
a9e63518e5 Merge branch 'CW-6125' into 'dev' 
Filter out unstranded annotations and log warning [CW-6125]

Closes CW-6125

See merge request epi2melabs/workflows/wf-transcriptomes!218
 2025-06-20 08:43:15 +00:00
Sarah Griffiths
85b767358c Filter out unstranded annotations and log warning [CW-6125] 2025-06-20 08:43:15 +00:00
Neil Horner
9f18c3f0d5 Merge branch 'container_update_CW-5998' into 'dev' 
Container update CW-5998

See merge request epi2melabs/workflows/wf-transcriptomes!215
 2025-05-16 08:38:28 +00:00
Neil Horner
b2ac1edbb9 Container update CW-5998 2025-05-16 08:38:28 +00:00
Neil Horner
2df9061a48 Merge branch 'alias_hyphens_CW-5484' into 'dev' 
Fix hyphens in sample alias CW-5484

See merge request epi2melabs/workflows/wf-transcriptomes!212
 2025-05-14 13:55:02 +00:00
Neil Horner
19b54ba2ff Fix hyphens in sample alias CW-5484 2025-05-14 13:55:01 +00:00
Neil Horner
bb47d92ac2 Merge branch 'TU_5.6.1' into 'dev' 
Tu 5.6.1 [CW-6099]

See merge request epi2melabs/workflows/wf-transcriptomes!214
 2025-05-09 07:05:35 +00:00
Neil Horner
c84a197da5 Tu 5.6.1 [CW-6099] 2025-05-09 07:05:34 +00:00
Neil Horner
1b3f49a1ac Merge branch 'template_update_5.6.0' into 'dev' 
Template update 5.6.0 [CW-6070]

See merge request epi2melabs/workflows/wf-transcriptomes!213
 2025-05-06 10:23:01 +00:00
Neil Horner
18bf1d5b19 Template update 5.6.0 [CW-6070] 2025-05-06 10:23:01 +00:00
Sarah Griffiths
a74a34763e Merge branch 'memory_mac_ci' into 'dev' 
memory ci config

See merge request epi2melabs/workflows/wf-transcriptomes!211
 2025-04-15 11:20:42 +00:00
Sarah Griffiths
11c9221edc memory ci config 2025-04-15 11:20:42 +00:00
Sarah Griffiths
1d76e7326e Merge branch 'CW-5950' into 'dev' 
Fix aws/docker demo cmd [CW-5950]

Closes CW-5950

See merge request epi2melabs/workflows/wf-transcriptomes!210
 2025-04-11 13:22:49 +00:00
Sarah Griffiths
00c2e9a18b Fix aws/docker demo cmd [CW-5950] 2025-04-11 13:22:48 +00:00
Sarah Griffiths
cd97c1398e Merge branch 'CW-5911' into 'dev' 
Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911]

Closes CW-5911

See merge request epi2melabs/workflows/wf-transcriptomes!209
 2025-04-03 12:57:58 +00:00
Sarah Griffiths
390739cf8a Output BAMS in all cases apart from transcriptome-source precomputed [CW-5911] 2025-04-03 12:57:58 +00:00
Sarah Griffiths
6f91cf59b1 Merge branch 'CW-5858' into 'dev' 
fix memory issue by replacing seq alignment stats with flagstat [CW-5858]

Closes CW-5858

See merge request epi2melabs/workflows/wf-transcriptomes!208
 2025-03-31 09:20:36 +00:00
Sarah Griffiths
c1f784ad04 fix memory issue by replacing seq alignment stats with flagstat [CW-5858] 2025-03-31 09:20:35 +00:00
Sarah Griffiths
60ec205339 Merge branch 'CW-5786' into 'dev' 
Only use exons in DE analysis [CW-5786]

Closes CW-5786

See merge request epi2melabs/workflows/wf-transcriptomes!207
 2025-03-28 09:58:05 +00:00
Sarah Griffiths
d5de051fd4 Only use exons in DE analysis [CW-5786] 2025-03-28 09:58:05 +00:00
Sarah Griffiths
9900143122 Merge branch 'CW-2965' into 'dev' 
Error message if ref_genome and ref_annotation mismatch CW-2965

Closes CW-2965

See merge request epi2melabs/workflows/wf-transcriptomes!202
 2025-03-14 19:06:47 +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
9ecd1345e9 Merge branch 'temp-update' into 'dev' 
Template v5.5.0 updates

See merge request epi2melabs/workflows/wf-transcriptomes!205
 2025-03-14 11:04:19 +00:00
Sarah Griffiths
b4bba1432b Template v5.5.0 updates 2025-03-14 11:04:18 +00:00
Chris Wright
9701041ce5 Merge branch 'fixup-docs' into 'dev' 
remove spaces in {{ ref_genome file }} in docs

See merge request epi2melabs/workflows/wf-transcriptomes!203
 2025-03-04 18:20:49 +00:00
Chris Wright
d2c1db81e8
remove spaces in {{ ref_genome file }} in docs 2025-03-04 16:24:06 +00:00
Neil Horner
350cb8d23b Merge branch 'missing_file_CW-5556' into 'dev' 
Fix overwritten DGE results file

See merge request epi2melabs/workflows/wf-transcriptomes!199
 2025-02-18 17:05:45 +00:00
Neil Horner
b62722751f Fix overwritten DGE results file 2025-02-18 17:05:45 +00:00
Natalia Garcia
205ff5ca59 Merge branch 'cw-5563-wf-transcriptomes' into 'dev' 
Update workflow tags [CW-5563]

See merge request epi2melabs/workflows/wf-transcriptomes!201
 2025-02-13 23:39:09 +00:00
Natalia Garcia
122ad8403a Update workflow tags [CW-5563] 2025-02-13 23:39:09 +00:00
Kiah McIntosh
428e337e22 Merge branch 'cw-3398' into 'dev' 
Use args for R script inputs [CW-3398]

See merge request epi2melabs/workflows/wf-transcriptomes!200
 2025-02-07 08:42:49 +00:00
Kiah McIntosh
eab8ef1efe Use args for R script inputs [CW-3398] 2025-02-07 08:42:49 +00:00
Neil Horner
91a514abd2 Merge branch 'schema_updates_CW-5529' into 'dev' 
Update schema

See merge request epi2melabs/workflows/wf-transcriptomes!197
 2025-01-23 10:59:32 +00:00
Neil Horner
e534921877 Update schema 2025-01-23 10:59:31 +00:00
Matt Parker
632a8f85a2 Merge branch 'split_bam_mem_CW-5352' into 'dev' 
Update memory for split_bam and  build_minimap_index_transcriptome

Closes CW-5352

See merge request epi2melabs/workflows/wf-transcriptomes!195
 2025-01-03 17:06:38 +00:00
Neil Horner
937a41f2cc Update memory for split_bam and build_minimap_index_transcriptome 2025-01-03 17:06:38 +00:00
Matt Parker
a33f3b967c Merge branch 'bump_v1.6.1' into 'dev' 
bump version

See merge request epi2melabs/workflows/wf-transcriptomes!196
 2025-01-03 12:44:09 +00:00
Neil Horner
39ef6ab16a bump version 2025-01-03 12:44:08 +00:00
Neil Horner
724a6515ea Merge branch 'empty_gff_CW-5438' into 'dev' 
Empty GFF bug CW-5438

See merge request epi2melabs/workflows/wf-transcriptomes!194
 2024-12-18 15:01:34 +00:00
Neil Horner
0ec44d03bd Empty GFF bug CW-5438 2024-12-18 15:01:33 +00:00
Matt Parker
74c19f1ea5 Merge branch 'bump_v1.6.0' into 'dev' 
Bump V1.6.0

See merge request epi2melabs/workflows/wf-transcriptomes!193
 2024-12-13 13:11:56 +00:00
Neil Horner
7ca3110648 Bump V1.6.0 2024-12-13 13:11:56 +00:00
Neil Horner
cb00ede5d8 Merge branch 'CW-5398' into 'dev' 
Access to undefined channel output bug CW-5398

Closes CW-5398

See merge request epi2melabs/workflows/wf-transcriptomes!192
 2024-12-13 11:51:07 +00:00
Neil Horner
c8c5922965 Access to undefined channel output bug CW-5398 2024-12-13 11:51:04 +00:00
Neil Horner
4c46f88f00 Merge branch 'gene_assignment_CW-5416' into 'dev' 
Account for stringtie multigene transcript artefacts

Closes CW-5369

See merge request epi2melabs/workflows/wf-transcriptomes!189
 2024-12-12 14:30:32 +00:00
Neil Horner
0a5c39cdf4 Account for stringtie multigene transcript artefacts 2024-12-12 14:30:31 +00:00
Neil Horner
112e87ad94 Merge branch 'template_2024_12_02' into 'dev' 
template update

See merge request epi2melabs/workflows/wf-transcriptomes!191
 2024-12-05 10:26:26 +00:00
Neil Horner
d38c7f3661 template update 2024-12-05 10:26:25 +00:00
Neil Horner
474c0fae3b Merge branch 'template_update_dec24' into 'dev' 
Update permissions

See merge request epi2melabs/workflows/wf-transcriptomes!190
 2024-12-02 12:55:51 +00:00