kfukuta/wf-transcriptomes-v202
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175 Commits 1 Branch 1 Tag 73 MiB
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Author SHA1 Message Date
Julian Libiseller-Egger
136ece6a90 update manifest description to match workflow card in app 2022-12-05 21:04:41 +00:00
Sarah Griffiths
93f95f7b4b Merge branch 'tag' into 'dev' 
tag

See merge request epi2melabs/workflows/wf-transcriptomes!87
 2022-12-01 22:12:44 +00:00
Sarah Griffiths
d3e48d4278 tag 2022-12-01 21:41:36 +00:00
Sarah Griffiths
9f2477e8c4 Merge branch 'schema-updates' into 'dev' 
schema updates

See merge request epi2melabs/workflows/wf-transcriptomes!86
 2022-12-01 21:05:01 +00:00
Sarah Griffiths
43e746f0ea schema updates 2022-12-01 21:05:01 +00:00
Sarah Griffiths
14ee337036 Merge branch 'CW-1170' into 'dev' 
CW-1170 Fix failed to plot

See merge request epi2melabs/workflows/wf-transcriptomes!78
 2022-11-16 20:11:50 +00:00
Sarah Griffiths
5477e721a2 CW-1170 Fix failed to plot 2022-11-16 20:11:44 +00:00
Sarah Griffiths
f852dde6ef Merge branch 'data-aws' into 'dev' 
Move data to AWS

See merge request epi2melabs/workflows/wf-transcriptomes!81
 2022-11-16 18:50:02 +00:00
Sarah Griffiths
5de212cf57 Move data to AWS 2022-11-16 18:49:53 +00:00
Sarah Griffiths
9a8b197ef0 Merge branch 'CW-1162' into 'dev' 
CW-1162 option to run DE without assembly transcriptome

See merge request epi2melabs/workflows/wf-transcriptomes!79
 2022-11-16 12:17:04 +00:00
Sarah Griffiths
cd1f97de4e CW-1162 option to run DE without assembly transcriptome 2022-11-16 12:16:38 +00:00
Neil Horner
7040a043d4 Merge branch 'jaffal_crash' into 'dev' 
Fix for when JAFFAL returns exit status 1 when no fusions are found

See merge request epi2melabs/workflows/wf-transcriptomes!80
 2022-11-15 19:56:48 +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
10b3253bad Merge branch 'CW-1167' into 'dev' 
CW-1167: error if conditionsheet and sample sheet dont match

See merge request epi2melabs/workflows/wf-transcriptomes!77
 2022-11-15 14:59:54 +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
248ecdb55b Merge branch 'CW-1044' into 'dev' 
demo data de

See merge request epi2melabs/workflows/wf-transcriptomes!76
 2022-11-08 18:07:49 +00:00
Sarah Griffiths
0758f4ab51 demo data de 2022-11-08 18:07:44 +00:00
Neil Horner
acfad92017 Merge branch 'fix_sha' into 'dev' 
Template changes

See merge request epi2melabs/workflows/wf-transcriptomes!75
 2022-10-07 12:59:19 +00:00
Neil Horner
d537d7b33f Template changes 2022-10-07 12:59:18 +00:00
Neil Horner
c8b474ef1a Merge branch 'version_bump' into 'dev' 
Verison bump

See merge request epi2melabs/workflows/wf-transcriptomes!74
 2022-08-24 13:28:43 +00:00
Neil Horner
d8834b7573 Verison bump 2022-08-24 11:38:20 +01:00
Neil Horner
835385e6af Merge branch '649-b' into 'dev' 
CW-649

See merge request epi2melabs/workflows/wf-transcriptomes!72
 2022-08-23 19:15:47 +00:00
Sarah Griffiths
c6b6121491 CW-649 2022-08-23 19:15:46 +00:00
Neil Horner
b140d3791e Merge branch 'transcript_table_threshold' into 'dev' 
Switch isoform table thresholding to just displaying to n rows based on coverage

See merge request epi2melabs/workflow-containers/wf-transcriptomes!73
 2022-08-08 13:48:15 +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
fad574dacf Merge branch 'pychopper_report_move' into 'dev' 
Move pychopper report up to qc section

See merge request epi2melabs/workflow-containers/wf-transcriptomes!69
 2022-08-04 15:46:56 +00:00
Neil Horner
f481daad09 Move pychopper report up to qc section 2022-08-04 15:46:55 +00:00
Neil Horner
c671a53a72 Merge branch 'disable_dag' into 'dev' 
Update nextflow.config

See merge request epi2melabs/workflow-containers/wf-transcriptomes!65
 2022-08-02 14:57:56 +00:00
Neil Horner
66a2b3aae0 Merge branch 'fusions' into 'dev' 
Fusions

See merge request epi2melabs/workflow-containers/wf-transcriptomes!64
 2022-08-01 19:07:20 +00:00
Neil Horner
e63cc73b6c Fusions 2022-08-01 19:07:20 +00:00
Neil Horner
d6f76de4f4 Update nextflow.config 2022-08-01 16:13:32 +00:00
Neil Horner
3614a1158a Merge branch 'fusions' into 'dev' 
Fusions

See merge request epi2melabs/workflow-containers/wf-transcriptomes!56
 2022-08-01 12:01:01 +00:00
Neil Horner
956c80573a Fusions 2022-08-01 12:01:01 +00:00
Neil Horner
be28906ab2 Merge branch 'CW-816-add-demo-data-to-each-workflow' into 'dev' 
Update nextflow_schema.json

See merge request epi2melabs/workflow-containers/wf-isoforms!62
 2022-07-27 14:35:41 +00:00
Thomas Rich
7a61c04ed9 Update nextflow_schema.json 2022-07-27 14:35:40 +00:00
Neil Horner
23c2e96939 Merge branch 'ci_config' into 'dev' 
nf-core lint fixes

See merge request epi2melabs/workflow-containers/wf-isoforms!61
 2022-07-26 09:54:32 +00:00
Neil Horner
f01b879be9 nf-core lint fixes 2022-07-26 09:54:32 +00:00
Matt Parker
619fe5bef5 Merge branch 'metamap-fastqingress' into 'dev' 
metamap-fastqingress

See merge request epi2melabs/workflow-containers/wf-isoforms!59
 2022-07-21 14:30:58 +00:00
Matt Parker
0f38613c6a metamap-fastqingress 2022-07-21 12:28:45 +01:00
Chris Wright
63d1d894ee Merge branch 'fq2fa' into 'dev' 
Skip fastq>a conversion

See merge request epi2melabs/workflow-containers/wf-isoforms!58
 2022-07-14 09:08:45 +00:00
Chris Wright
1ab5e2744c Skip fastq>a conversion 2022-07-14 09:08:44 +00:00
Neil Horner
3efcf30a34 Merge branch 'CW-790' into 'dev' 
template updates

Closes CW-790

See merge request epi2melabs/workflow-containers/wf-isoforms!57
 2022-07-07 19:14:52 +00:00
Sarah Griffiths
fa1818a81d template updates 2022-07-07 19:14:52 +00:00
Neil Horner
b44ec7d98d Merge branch 'epi2melabs_pychopper' into 'dev' 
Epi2melabs pychopper

See merge request epi2melabs/workflow-containers/wf-isoforms!54
 2022-06-01 12:08:00 +00:00
Neil Horner
d97e84cdc1 Epi2melabs pychopper 2022-06-01 12:08:00 +00:00
Matt Parker
2f2130b443 Merge branch 'ignore-wf' into 'dev' 
ignore wf param

See merge request epi2melabs/workflow-containers/wf-isoforms!53
 2022-05-26 11:36:19 +00:00
Matt Parker
e9d750bcee ignore wf param 2022-05-26 10:40:51 +01:00
Matt Parker
b7efda8e16 Merge branch 'new-ci-rules' into 'dev' 
Implementing SN new CI rules

See merge request epi2melabs/workflow-containers/wf-isoforms!52
 2022-05-26 09:33:45 +00:00
Matt Parker
79a4bec16d Zero hour 9:00 a.m. 2022-05-26 08:27:38 +01:00
Neil Horner
ebf814b4e2 Merge branch 'gh_8' into 'dev' 
Github issues

See merge request epi2melabs/workflow-containers/wf-isoforms!51
 2022-04-11 15:08:47 +00:00