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1281 commits

Author SHA1 Message Date
Michael Borg
cc380ce9a1
Update mpcdf.config
Added polling frequencies to the config as requested by MPCDF admin. Also updated the number of (real) cores on Raven.
2022-02-02 13:33:03 +01:00
Harshil Patel
9792226f5c
Update genomes.config 2022-01-27 12:45:41 +00:00
Harshil Patel
c49abc2e61
Merge pull request #316 from drpatelh/nextclade
Add --nextclade_dataset params
2022-01-17 17:35:31 +00:00
Harshil Patel
cd6b8e0f17 Add --nextclade_dataset params 2022-01-17 16:51:55 +00:00
Harshil Patel
a680207b55
Merge pull request #315 from drpatelh/nextclade
Add Nextclade genome details to viralrecon genome config
2022-01-17 11:46:47 +00:00
Harshil Patel
f26c465bd4 Add Nextclade genome details to viralrecon genome config 2022-01-17 11:27:10 +00:00
James A. Fellows Yates
4546e0f389
Merge pull request #314 from jfy133/master
Update eager@eva to add java buffer for bbduk
2022-01-14 07:40:56 +01:00
James A. Fellows Yates
5fd5c43906
Update eva.config 2022-01-14 07:03:05 +01:00
Maxime U. Garcia
61682f33b3
Merge pull request #310 from nf-core/praveenraj2018-patch-1
Updated sentieon version through a new module file
2022-01-10 12:04:20 +01:00
ameynert
bfa7e0f8d7
Merge pull request #313 from nf-core/ameynert-patch-1
Added memory & cluster options specification for eddie sarek config
2022-01-06 10:38:13 +00:00
ameynert
0f56588acc
Added memory & cluster options specification for eddie sarek config 2022-01-06 10:15:34 +00:00
praveenraj2018
53ab5ee34f
Updated sentieon version through a new module file
A local module file has been created to run the latest version of Sentieon. Doing this change, as the new version of Sentieon has only a dependency library update, hence it should not break the Sentieon pipeline. Tested locally with a test.conf having the new process block.
2021-12-21 15:21:59 +01:00
Kevin Brick
1abb1c2d95
Merge pull request #309 from kevbrick/master
Added config for NIH Biowulf Cluster
2021-12-20 13:05:19 -05:00
Kevin Brick
82c7d553a7
Update bind-paths 2021-12-20 11:29:09 -05:00
Kevin Brick
afb6fbb767
Trailing spaces 2021-12-17 00:46:50 -05:00
Kevin Brick
05f7b59573
Update nihbiowulf.md 2021-12-17 00:44:39 -05:00
Kevin Brick
74448de49e
Update main.yml
add nihbiowulf
2021-12-17 00:40:43 -05:00
Kevin Brick
e523e28861
Update README.md 2021-12-17 00:39:21 -05:00
Kevin Brick
de6d3bdd5f
Update nfcore_custom.config 2021-12-17 00:38:07 -05:00
Kevin Brick
9cf4f69ff3
Add files via upload 2021-12-17 00:37:11 -05:00
Kevin Brick
87e4ece034
Add files via upload 2021-12-17 00:36:51 -05:00
Venkat Malladi
38295dfbbd
Merge pull request #308 from vsmalladi/master
Fix name of Params
2021-12-16 14:11:53 -06:00
Venkat Malladi
306c802b4e
Fix name of Params 2021-12-16 09:27:23 -06:00
Maxime U. Garcia
58fe1a5808
Merge pull request #307 from nf-core/praveenraj2018-patch-1
Renamed star_index directory
2021-12-14 21:38:15 +01:00
praveenraj2018
00a3ed0fa6
Formatting 2021-12-14 21:24:18 +01:00
praveenraj2018
0557f4e062
Renamed star_index directory 2021-12-14 21:15:12 +01:00
praveenraj2018
e4410065f3
Merge pull request #306 from praveenraj2018/rnavar_munin
Added rnavar pipeline config for Munin
2021-12-14 16:10:59 +01:00
Maxime U. Garcia
5e92e2ef11
Update conf/pipeline/rnavar/munin.config 2021-12-14 16:10:31 +01:00
Praveen
4c6e7262c2 Updated README.md 2021-12-14 04:04:17 +01:00
Praveen
cc1fe5b5a0 Addressed review feedback 2021-12-14 03:58:54 +01:00
Praveen
b4d5330c0e Added rnavar pipeline config for Munin 2021-12-14 03:52:37 +01:00
James A. Fellows Yates
71b17ff970
Merge pull request #301 from jfy133/eva
eager@eva: and bump the second samtools_flagstat process overhead 🙄
2021-12-07 11:04:33 +01:00
James A. Fellows Yates
55f452d81e
Update eva.config 2021-12-07 09:27:28 +01:00
James A. Fellows Yates
f7b5a8e800
Merge pull request #300 from jfy133/eva
eager @ eva: reintroduce bionode8, bump overhead for flagstat
2021-12-03 11:16:24 +01:00
James Fellows Yates
e8252ad61c Reintroduce bionode8, bump overhead for flagstat 2021-12-03 08:36:31 +01:00
James A. Fellows Yates
f8246b8554
Merge pull request #299 from jfy133/eva
Exclude bionode8 for eager@eva
2021-12-02 10:57:44 +01:00
James Fellows Yates
06b40798c0 Exclude bionode8 2021-12-02 10:35:35 +01:00
Venkat Malladi
7a49a66b36
Merge pull request #298 from vsmalladi/azure
Fix Azure Markdown
2021-11-18 23:52:24 -06:00
Venkat Malladi
d722e7206e Fix readme to remove blob account. 2021-11-18 18:06:54 -06:00
Venkat Malladi
c0bf71bb6c Merge branch 'master' into azure 2021-11-18 18:06:04 -06:00
Phil Ewels
0725e8d382
Merge pull request #225 from jfy133/doc-update
Make more explicit which files you must update
2021-11-19 00:56:50 +01:00
Phil Ewels
4785ceccba
Merge pull request #245 from ikeller/unibe_ibu
Unibe ibu
2021-11-19 00:56:25 +01:00
Phil Ewels
291fcb20a5
Merge pull request #297 from vsmalladi/azure
Add in template for Azure Workflow
2021-11-19 00:55:54 +01:00
Venkat Malladi
1312949768 Merge branch 'azure' of github.com:vsmalladi/configs into azure 2021-11-18 17:55:37 -06:00
Venkat Malladi
46182c7439 Fix markdown linting erros. 2021-11-18 17:55:16 -06:00
Phil Ewels
b25bd1ce42
Update docs/azurebatch.md 2021-11-19 00:54:39 +01:00
Venkat Malladi
72ccd44ad6 Remove storage name. 2021-11-18 17:52:51 -06:00
Venkat Malladi
ed4c1d5f22 Remove work_dir option. 2021-11-18 17:52:24 -06:00
Phil Ewels
286fa6753a
Apply suggestions from code review 2021-11-19 00:07:33 +01:00
Phil Ewels
e090bbd5fe
Merge pull request #241 from asafpr/master
replaced owner in JAX
2021-11-19 00:03:11 +01:00