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Author SHA1 Message Date
Thiseas C. Lamnidis
fa4075c2a0
Removed all time limits 2022-02-10 10:00:18 +01:00
James A. Fellows Yates
64355b84d2
Merge pull request #325 from jfy133/eva-update 
Read add empty BAM exit code for qualimap 255 for eager @ EVA
 2022-02-08 11:28:36 +01:00
James A. Fellows Yates
2b06293f64
Read add empty BAM exit code for qualitmap 255 2022-02-08 11:15:17 +01:00
James A. Fellows Yates
8d286e3b69
Merge pull request #324 from jfy133/eva-update 
New attempt of workaround SGE + Java incompatibility for eager @ EVA
 2022-02-06 20:02:03 +01:00
James A. Fellows Yates
8c5a54ac9f
Update conf/pipeline/eager/eva.config 2022-02-06 19:37:53 +01:00
James A. Fellows Yates
aa525c6ebf
Allow exit code 1 retry for all java processes 2022-02-06 09:07:53 +01:00
Patrick Hüther
8ff6f302b4
Merge pull request #320 from rbpisupati/cbe-singularity 
cbe: update config and docs
 2022-02-04 10:40:16 +01:00
phue
7bf6f284fa cbe: lower the threshold for switching to m queue 2022-02-04 10:33:00 +01:00
phue
49810a69b3 cbe: add gpu support 
just in case.. note that this will need --nv in containerOptions in order to mount cuda libs into the container
 2022-02-04 10:31:58 +01:00
phue
a6dd3aa0f1 cbe: update recommended nextflow version in docs 
otherwise, the new anaconda requirements will cause conflicts
 2022-02-04 10:21:52 +01:00
phue
52b6f7da21 update anaconda module 
not sure why a binary distribution needs a buildenv at all, but well
 2022-02-04 10:18:59 +01:00
phue
c3db683535 Merge branch 'master' of github.com:nf-core/configs into cbe-singularity 2022-02-04 10:14:52 +01:00
phue
b5ab4a8258 Revert "changes to cbe module loading" 
This reverts commit 7c1c4c7fa4.
 2022-02-04 10:13:12 +01:00
James A. Fellows Yates
81fe720b00
Update eva.config 2022-02-04 09:31:33 +01:00
James A. Fellows Yates
86a9042eac
Update eva.config 2022-02-04 09:25:01 +01:00
James A. Fellows Yates
50aafc6410
Update eva.config 2022-02-03 17:03:10 +01:00
rbpisupati
7c1c4c7fa4 changes to cbe module loading 2022-02-02 22:42:13 +01:00
James A. Fellows Yates
8739aabbf0
Bump markduplicates by default 2022-02-02 08:00:13 +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