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107 Commits

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Author SHA1 Message Date
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
Neil Horner
3030ccbbdf Updated version in schema 2022-02-07 11:56:42 +00:00
Neil Horner
4a978c1a4c Merge branch 'release_0.1.0_fix' into 'dev' 
Addded 'v' to changelog version

See merge request epi2melabs/workflow-containers/wf-isoforms!37
 2022-02-07 11:44:44 +00:00
Neil Horner
a7568c00b7 Addded v to changelog version 2022-02-07 11:36:25 +00:00
Neil Horner
ddca3e6208 Merge branch 'denovo3' into 'dev' 
Merge de novo pipeline

Closes #1

See merge request epi2melabs/workflow-containers/wf-isoforms!35
 2022-01-26 15:54:59 +00:00
Neil Horner
5dfbb0f38a Merge de novo pipeline 2022-01-26 15:54:55 +00:00
Thomas Rich
391b5d5c84 Merge branch 'update-schema' into 'dev' 
Update nextflow_schema.json

See merge request epi2melabs/workflow-containers/wf-isoforms!32
 2022-01-11 16:04:22 +00:00
Thomas Rich
151ef46522 Update nextflow_schema.json 2022-01-11 16:04:22 +00:00
Neil Horner
de3edcb31e Merge branch 'port_from_snakemake' into 'dev' 
Initial port of ref-isoforms to Nextflow

Closes #1

See merge request epi2melabs/workflow-containers/wf-isoforms!31
 2021-12-08 14:34:18 +00:00
Neil Horner
458ac5d274 Initial port of ref-isoforms to Nextflow 2021-12-08 14:34:07 +00:00
Chris Wright
4a1b5cd50b Merge branch 'schema' into 'dev' 
add schema

See merge request epi2melabs/workflow-containers/wf-template!25
 2021-09-29 09:51:37 +00:00
Chris Wright
6f6ff11257 Merge branch 'remoteinputs' into 'dev' 
Support s3 input paths

See merge request epi2melabs/workflow-containers/wf-template!26
 2021-09-29 09:51:32 +00:00
Chris Wright
038d399b12 Support s3 input paths 2021-09-28 17:11:33 +01:00
Chris Wright
e486b98a2c add schema 2021-09-28 15:11:18 +01:00
Sarah Griffiths
0d230e3930 Merge branch 'align-parameters' into 'dev' 
align parameters

See merge request epi2melabs/workflow-containers/wf-template!24
 2021-09-10 14:19:24 +00:00
Sarah Griffiths
2be5b01cc8 align parameters 2021-09-10 13:59:43 +00:00
Sarah Griffiths
c8c79a6a36 Merge branch 'CW-244' into 'dev' 
CW-244 optional report name

Closes CW-244

See merge request epi2melabs/workflow-containers/wf-template!23
 2021-09-09 13:39:17 +00:00
Sarah Griffiths
167deee265 CW-244 optional report name 2021-09-09 13:39:17 +00:00
Sarah Griffiths
d030e654e9 Merge branch 'CW-247' into 'dev' 
CW-247 error on no fastq

Closes CW-247

See merge request epi2melabs/workflow-containers/wf-template!22
 2021-09-09 10:15:34 +00:00
Sarah Griffiths
fb0230358f Update fastqingress.nf to give error message if no fastq files 2021-09-08 13:42:51 +00:00
Thomas Rich
62425e1d89 Merge branch 'add-params-table' into 'dev' 
Add params table in report and process

See merge request epi2melabs/workflow-containers/wf-template!20
 2021-08-19 14:48:39 +00:00
Amber Wright
fe03715e6b Merge branch 'duplicate_dockerignore_entry' into 'dev' 
Update .dockerignore duplicate entry

See merge request epi2melabs/workflow-containers/wf-template!21
 2021-07-29 13:23:39 +00:00
Amber Wright
3ac6cc9768 Update .dockerignore duplicate entry 2021-07-29 13:18:18 +00:00
Karhide
ca5111b287 Add params table in report and process 2021-07-29 12:32:19 +01:00
Chris Wright
ab1706603b Bump version 2021-07-28 17:30:27 +00:00
Chris Wright
621e910c5d Merge branch 'mamba' into 'dev' 
Switch conda profile to use mamba

See merge request epi2melabs/workflow-containers/wf-template!19
 2021-07-27 13:45:22 +00:00
Chris Wright
fcc1394600 Switch conda profile to use mamba 2021-07-27 11:19:11 +01:00
Chris Wright
0f19083e57 Bump default BASEIMAGE 2021-07-26 11:18:43 +00:00
Chris Wright
16f41f778f Update LICENSE 2021-07-26 09:51:41 +00:00
Chris Wright
b7fbb9d1fe Merge branch 'dev' into makesmaller 2021-07-23 17:39:26 +01:00
Chris Wright
8afc348434 Fix version file passing 2021-07-23 17:34:46 +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
eef235b8ce Optimise image size a little 2021-07-22 17:37:02 +01:00
Chris Wright
527307b0e5 Merge branch 'stripreadme' into 'dev' 
Cut down readme to workflow particulars

See merge request epi2melabs/workflow-containers/wf-template!15
 2021-07-22 14:35:11 +00:00
Chris Wright
49ba6effd6 Merge branch 'samples' into 'dev' 
add fastqingress module

See merge request epi2melabs/workflow-containers/wf-template!14
 2021-07-22 14:00:50 +00:00
Chris Wright
48a985f7c3 Cut down readme to workflow particulars 2021-07-22 13:55:44 +01:00
Chris Wright
2a1ff88cc7 add fastqingress module 2021-07-12 21:15:03 +01:00
Chris Wright
ee30d5bb7c Merge branch 'testnewmamba' into 'dev' 
Testnewmamba

See merge request epi2melabs/workflow-containers/wf-template!13
 2021-06-30 16:59:26 +00:00
Chris Wright
feb1c5e9fd Testnewmamba 2021-06-30 16:59:26 +00:00
Chris Wright
c11f0f214b Update nextflow.config, CHANGELOG.md files 2021-05-17 15:21:42 +01:00
Chris Wright
7e013608f9 Remove macos run 2021-04-29 16:16:33 +01:00
Chris Wright
57ff953621 mac docker 2021-04-29 16:04:48 +01:00
Chris Wright
0e12112439 Merge branch 'versions' into 'dev' 
Add version report

See merge request epi2melabs/workflow-containers/wf-template!12
 2021-04-29 14:52:21 +01:00
Chris Wright
c65c752277 Add version report 2021-04-29 14:52:21 +01:00
Chris Wright
6ee6f171d8 Tidy up and add mock optional file example 2021-04-13 11:46:44 +01:00
Chris Wright
62afff20c4 Add aws batch profile 2021-03-29 18:10:53 +01:00