kfukuta/wf-transcriptomes-v202
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131 Commits

Author SHA1 Message Date
Neil Horner
b2ac1edbb9 Container update CW-5998 2025-05-16 08:38:28 +00:00
Neil Horner
19b54ba2ff Fix hyphens in sample alias CW-5484 2025-05-14 13:55:01 +00:00
Neil Horner
18bf1d5b19 Template update 5.6.0 [CW-6070] 2025-05-06 10:23:01 +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
d5de051fd4 Only use exons in DE analysis [CW-5786] 2025-03-28 09:58:05 +00:00
Sarah Griffiths
b4bba1432b Template v5.5.0 updates 2025-03-14 11:04:18 +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
Kiah McIntosh
eab8ef1efe Use args for R script inputs [CW-3398] 2025-02-07 08:42:49 +00:00
Neil Horner
c8c5922965 Access to undefined channel output bug CW-5398 2024-12-13 11:51:04 +00:00
Neil Horner
0a5c39cdf4 Account for stringtie multigene transcript artefacts 2024-12-12 14:30:31 +00:00
Neil Horner
624c16a3b1 Update permissions 2024-12-02 12:55:51 +00:00
Neil Horner
5c4780a1b2 Update report CW-3077 2024-10-25 15:18:05 +00:00
Sarah Griffiths
d83807f38d Tidy de analysis 2024-09-16 09:26:12 +00:00
Sarah Griffiths
7ced52c05b Template updates 2024-09-11 12:47:01 +00:00
Sam Nicholls
46363987aa Output dtu_plots to local work dir then mv [CW-4886] 2024-09-09 18:41:17 +00:00
Neil Horner
0200514536 Remove fusion detection [CW-4552] 2024-08-06 20:20:19 +00:00
Neil Horner
0f4eee002a template update 2024-07-10 2024-07-26 08:34:05 +00:00
Neil Horner
c662293317 Template update 2024-06-27 16:13:55 +01:00
Neil Horner
e2585dcd11 Template update 2024 05 24 2024-05-30 19:40:11 +00:00
Sarah Griffiths
d7fcb2d5f7 Temp update 2024-05-10 08:42:12 +00:00
Sarah Griffiths
63e0fe6524 change significance level to mark on MA plot 2024-04-10 08:09:23 +00:00
Sarah Griffiths
595aae4006 Template update 2024-04-03 09:47:29 +00:00
Sarah Griffiths
6a14a1d85b Remove need to retry based on GTF/GFF 2024-02-22 09:34:38 +00:00
Sarah Griffiths
e3b1967872 Improve ref annotation transcript id version handling 2024-02-19 10:29:04 +00:00
Sarah Griffiths
e30d3aec98 DE_analysis params change input types to numeric 2024-02-16 10:23:15 +00:00
Neil Horner
bb9acf55be Resolve CW-3468 "Incorrect ids" 2024-02-13 08:48:21 +00:00
Neil Horner
d5b0cc6203 JAFFAL resources 2024-02-12 15:25:19 +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
1be77ba77f CW-3075 improve counts output files 2024-02-02 10:38:50 +00:00
Neil Horner
92cb357edc Template updates 2024 01 12 2024-01-16 11:48:09 +00:00
Sarah Griffiths
b870078142 tag v0.4.2 2023-11-17 10:06:36 +00:00
Sarah Griffiths
e1b2a08918 control for sample sheet 2023-10-25 10:41:08 +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
fb718ac3f7 Update file check_sample_sheet.py 2023-09-01 16:03:19 +00:00
Sarah Griffiths
ab850ac67f tidy up DE outputs 2023-08-10 10:05:11 +00:00
Sarah Griffiths
ec3c346fd8 fix and test for files with no gene id in attributes 2023-07-26 18:14:00 +00:00
Sarah Griffiths
a58d08b6c4 template updates 2023-07-25 08:33:01 +00:00
Sarah Griffiths
f86b74a494 CW-2217 fix ordering of sample_ids 2023-07-12 11:05:34 +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
5df7e3c2cd template updates 2023-05-09 10:09:33 +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
5477e721a2 CW-1170 Fix failed to plot 2022-11-16 20:11:44 +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
Sarah Griffiths
0758f4ab51 demo data de 2022-11-08 18:07:44 +00:00
Neil Horner
d8834b7573 Verison bump 2022-08-24 11:38:20 +01:00
Sarah Griffiths
c6b6121491 CW-649 2022-08-23 19:15:46 +00:00
Neil Horner
d477a747e6 Switch isoform table thresholding to just displaying to n rows based on coverage 2022-08-08 13:48:15 +00:00
Neil Horner
f481daad09 Move pychopper report up to qc section 2022-08-04 15:46:55 +00:00
Neil Horner
e63cc73b6c Fusions 2022-08-01 19:07:20 +00:00
Neil Horner
956c80573a Fusions 2022-08-01 12:01:01 +00:00
Neil Horner
d97e84cdc1 Epi2melabs pychopper 2022-06-01 12:08:00 +00:00
Neil Horner
3b69e64c4f Github issues 2022-04-11 15:08:47 +00:00
Neil Horner
b4fac77b11 Merge branch 'gh#8' into 'dev' 
Empty dataframe bug

Closes CW-603

See merge request epi2melabs/workflow-containers/wf-isoforms!49
 2022-04-07 12:57:38 +00:00
Neil Horner
39f478ceef Empty dataframe bug 2022-04-07 12:57:38 +00:00
Neil Horner
07275010c0 Fnames 2022-04-06 09:45:25 +00:00
Neil Horner
c2a0f8dc21 Re-add ability to do direct RNA 2022-04-05 18:04:16 +00:00
Neil Horner
4d91b738e1 Post cw460 2022-03-02 14:15:39 +00:00
Neil Horner
03b8ba51f6 Denovo bug fixes 2022-03-02 11:34:21 +00:00
Neil Horner
7e33eb2c3b Moved fiterable table into aplanat and general tidy up 2022-02-28 14:17:46 +00:00
Neil Horner
5dfbb0f38a Merge de novo pipeline 2022-01-26 15:54:55 +00:00
Neil Horner
458ac5d274 Initial port of ref-isoforms to Nextflow 2021-12-08 14:34:07 +00:00
Karhide
ca5111b287 Add params table in report and process 2021-07-29 12:32:19 +01:00
Chris Wright
635b18121b Fix typos 2021-07-23 17:02:03 +01:00
Chris Wright
b61a1c0f5f Update version reporting 2021-07-23 16:49:32 +01:00
Chris Wright
2a1ff88cc7 add fastqingress module 2021-07-12 21:15:03 +01:00
Chris Wright
c65c752277 Add version report 2021-04-29 14:52:21 +01:00
Chris Wright
d1901bb16f rename report 2021-03-23 16:18:53 +00:00
Chris Wright
e8e584d451 Set fastq option straight 2021-03-19 11:22:10 +00:00
Chris Wright
3f99c88a9d Clean up bin 2021-03-17 11:24:07 +00:00
Chris Wright
ed1fc2c9fd Add larger test data and sample report 2021-03-01 11:44:41 +00:00
Chris Wright
5c60ad6779 Backport additions from wf-artic 2021-02-24 17:45:39 +00:00