kfukuta/wf-transcriptomes-v202
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203 Commits

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Author SHA1 Message Date
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
Neil Horner
3b69e64c4f Github issues 2022-04-11 15:08:47 +00:00
Neil Horner
00255c86f7 Merge branch 'docs' into 'dev' 
New docs format

See merge request epi2melabs/workflow-containers/wf-isoforms!50
 2022-04-08 16:33:50 +00:00
Neil Horner
e2f290b415 New docs format 2022-04-08 16:33:50 +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
0ac1054064 Merge branch 'fnames' into 'dev' 
Fnames

Closes CW-565

See merge request epi2melabs/workflow-containers/wf-isoforms!47
 2022-04-06 09:45:26 +00:00
Neil Horner
07275010c0 Fnames 2022-04-06 09:45:25 +00:00
Neil Horner
63c4b5c7a5 Merge branch 'direct_rna' into 'dev' 
Re-add ability to do direct RNA

Closes CW-566

See merge request epi2melabs/workflow-containers/wf-isoforms!46
 2022-04-05 18:04:17 +00:00
Neil Horner
c2a0f8dc21 Re-add ability to do direct RNA 2022-04-05 18:04:16 +00:00
Neil Horner
7dfea725a0 Merge branch 'clv0.1.1' into 'dev' 
bump CHANGELOG version

See merge request epi2melabs/workflow-containers/wf-isoforms!45
 2022-03-02 21:56:41 +00:00
Neil Horner
4ddc1f16ab bump CHANGELOG version 2022-03-02 19:50:29 +00:00
Neil Horner
778b769a9b Merge branch 'fix_output' into 'dev' 
Add  to output process

See merge request epi2melabs/workflow-containers/wf-isoforms!44
 2022-03-02 15:23:49 +00:00
Neil Horner
f45fa8f2f2 Add to output process 2022-03-02 15:08:06 +00:00
Neil Horner
0d3bd221f0 Merge branch 'post-cw460' into 'dev' 
Post cw460

See merge request epi2melabs/workflow-containers/wf-isoforms!43
 2022-03-02 14:15:39 +00:00
Neil Horner
4d91b738e1 Post cw460 2022-03-02 14:15:39 +00:00
Neil Horner
61573e1117 Merge branch 'cw-460' into 'dev' 
Denovo bug fixes

Closes CW-460

See merge request epi2melabs/workflow-containers/wf-isoforms!42
 2022-03-02 11:34:22 +00:00
Neil Horner
03b8ba51f6 Denovo bug fixes 2022-03-02 11:34:21 +00:00
Neil Horner
b56cec9994 Merge branch 'table_to_aplanat' into 'dev' 
Moved fiterable table into aplanat and general tidy up

See merge request epi2melabs/workflow-containers/wf-isoforms!36
 2022-02-28 14:17:46 +00:00
Neil Horner
7e33eb2c3b Moved fiterable table into aplanat and general tidy up 2022-02-28 14:17:46 +00:00
Neil Horner
8b1cc95433 Merge branch 'schema_split' into 'dev' 
Seperated out the params into logical sections

See merge request epi2melabs/workflow-containers/wf-isoforms!40
 2022-02-23 14:58:39 +00:00
Neil Horner
76fd8f9c81 Seperated out the params into logical sections 2022-02-23 14:58:39 +00:00
Neil Horner
4782a1473c Merge branch 'release_0.1.0_fix' into 'dev' 
Updated version in schema

See merge request epi2melabs/workflow-containers/wf-isoforms!38
 2022-02-07 14:24:20 +00:00