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783 commits

Author SHA1 Message Date
Praveen Raj S
9747d5fe15
Added PileupSummariesForMutect2 in CPU limit list 
Add PileupSummariesForMutect2 to the list to run with less threads.
Changed the MaxForks to 12
Tested on an internal sample and it worked!
 2022-03-16 14:36:25 +01:00
Alexander Peltzer
d510cb254e
Merge pull request #165 from ewels/fix-show-profiles 
Set params.custom_config_base in nextflow.config
 2022-03-15 17:13:24 +01:00
Praveen Raj S
a844335942
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:59:06 +01:00
Praveen Raj S
cb96c4bd2d
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:56:11 +01:00
Praveen Raj S
13c66f7e98
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:56:03 +01:00
Praveen Raj S
50c4610345
Adjusted time and maxforks for Mutect2 2022-03-15 16:29:19 +01:00
Alexander Peltzer
3e4fae71a4
Merge branch 'master' into fix-show-profiles 2022-03-15 14:52:29 +01:00
James A. Fellows Yates
1b5037ce5e
Update eva.config 2022-03-15 07:49:06 +01:00
James A. Fellows Yates
1565b2ce63
Update eva.config 2022-03-15 07:42:23 +01:00
James A. Fellows Yates
f725b6c431
Apply suggestions from code review 2022-03-15 07:36:34 +01:00
Nathan S. Watson-Haigh
a0f5ac7445
Added references subdir to igenomes_base 2022-03-15 11:41:51 +10:30
James A. Fellows Yates
4670f8bf0c
Update eva.config 2022-03-14 14:56:01 +01:00
James A. Fellows Yates
a2e2e94333
Merge pull request #344 from njspix/vai 
Add VAI configuration
 2022-03-14 14:36:00 +01:00
Nathan Watson-Haigh
cc55026751 Add singularity to PATH 2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh
2f0b022571 Fixed typos 2022-03-13 00:08:42 +10:30
Nathan Watson-Haigh
b638694bd0 Added SAHMRI HPC profile 2022-03-12 21:17:33 +10:30
Matiss
6c79c75eec
Merge pull request #290 from maxozo/master 
added leicester profile
 2022-03-11 09:21:09 +00:00
Nathan Spix
d067f61329
remove extra spaces 2022-03-07 15:22:18 -05:00
Spix
17c77ad516 update singularity command 2022-03-07 15:13:26 -05:00
Spix
c97c48ae5b update singularity command 2022-03-07 15:11:45 -05:00
Spix
429c7b4fa8 initial commit 2022-03-07 15:01:46 -05:00
Alexander Peltzer
d0d86bfb2a
Merge pull request #339 from jfy133/rnaseq_mpcdf 
Add RNASEQ specific config for MPCDF
 2022-03-07 13:59:08 +01:00
James A. Fellows Yates
975fca6721
Apply suggestions from code review 2022-03-07 13:51:00 +01:00
Natalia Zajac
97058995ef Update on singularity cache 2022-03-07 12:37:01 +01:00
Natalia Zajac
e07a0e548e Config Addition 2022-03-04 12:16:01 +01:00
James Fellows Yates
70318c3b2a Tweak eager settigs 2022-03-03 14:29:30 +01:00
James A. Fellows Yates
546393ed18
Apply suggestions from code review 2022-03-03 14:22:35 +01:00
ilight1542
5a0543e4ac
Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update 2022-03-03 14:17:18 +01:00
ilight1542
25c644abb7 modified mpcdf configs (general + eager) 2022-03-03 13:55:02 +01:00
James Fellows Yates
7112e74b73 Tweak settings based on latest batch specs 2022-03-03 13:43:40 +01:00
James A. Fellows Yates
17312604cf
Update mpcdf.config 2022-03-03 12:25:06 +01:00
James Fellows Yates
94f8cbcb84 Add rnaseq pipeline specific config for MPCDF 2022-03-03 12:20:02 +01:00
James A. Fellows Yates
5547e45ab5
Merge branch 'master' into jfy133-patch 2022-03-02 08:28:22 +01:00
James A. Fellows Yates
ea052a7b67
Merge pull request #334 from jfy133/eva-update 
eva: generalise custom SGE mem flag
 2022-03-01 09:23:04 +01:00
James A. Fellows Yates
a6c12d8edc
Merge pull request #322 from U-BDS/master 
Add UAB Cheaha profile
 2022-03-01 08:29:54 +01:00
PCQ
1ff92db608
Merge branch 'nf-core:master' into master 2022-02-28 14:50:41 +01:00
James A. Fellows Yates
89f6484325
Merge pull request #319 from maltesemike/patch-2 
Update mpcdf.config
 2022-02-28 14:06:06 +01:00
James A. Fellows Yates
46f046d477
Update eva.config 2022-02-28 14:00:37 +01:00
James A. Fellows Yates
d7d9951dbf
Insert h_vmem for all nf-core pipelines 2022-02-28 14:00:16 +01:00
James A. Fellows Yates
6210ee874c
Update eva.config 2022-02-28 13:57:37 +01:00
Mei Wu
dcba537d15 picard md is single threaded 2022-02-21 16:19:17 +01:00
Maxime U. Garcia
41e00ae8f9
Update conf/munin.config 2022-02-14 13:11:46 +01:00
Praveen Raj S
90936a5518
Added: runOptions to singularity 
To bind external mount directories at runtime.
 2022-02-14 12:45:20 +01:00
Combiz Khozoie
2d434c6ee5
Merge pull request #321 from nf-core/combiz-patch-1 
Imperial config updates
 2022-02-11 14:49:30 +00:00
Maxime U. Garcia
4a936a685e
Merge pull request #317 from nf-core/praveenraj2018-patch-1 
Added genome parameter
 2022-02-11 15:33:18 +01:00
Combiz Khozoie
a77f718ae2
Merge pull request #330 from nf-core/master 
Pulling master to branch
 2022-02-11 14:18:01 +00:00
Combiz Khozoie
3ce32f50c4
Update imperial.config 
Moved params configs from internal profile to universal
 2022-02-11 11:02:40 +00:00
Combiz Khozoie
b99b74b2d3
Update imperial.config 
Fixed indent
 2022-02-11 00:26:45 +00:00
Combiz Khozoie
38a05a6531
Update imperial.config 
Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
 2022-02-10 23:46:14 +00:00
Combiz Khozoie
e1d0bf0cd2
Delete imperial_mb.config 
Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config
 2022-02-10 23:44:49 +00:00
Combiz Khozoie
fe5474a029
Update imperial.config 
Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC
 2022-02-10 23:02:47 +00:00
Harshil Patel
8fa6ab9b35
Merge pull request #323 from stevin-wilson/patch-1 
Added ARTIC v4.1 primer set information
 2022-02-10 19:17:47 +00:00
James Fellows Yates
88ddc9eee7 fffff 2022-02-10 11:34:57 +01:00
James Fellows Yates
d7d0f5cecc Change base time 2022-02-10 11:32:49 +01:00
James Fellows Yates
dbd78f8075 Re add . 2022-02-10 11:26:18 +01:00
James Fellows Yates
dd94895f16 remove quotes 2022-02-10 11:22:45 +01:00
James Fellows Yates
39c2d9b25b Oops 2022-02-10 11:19:16 +01:00
James Fellows Yates
c0ee3225ad Add times for 365d 2022-02-10 11:02:52 +01:00
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
Stevin Wilson
dbb71161c5
Added ARTIC v4.1 primer set information 2022-02-04 15:31:51 -05:00
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
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
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
Combiz Khozoie
81a273c730
Update imperial_mb.config 
Dropped support for pqmedbio-large which is not currently available.
 2022-02-03 18:31:02 +00:00
Combiz Khozoie
2bdf5863d9
Update imperial.config 
Removed my contact details.  Users can request help on the nf-core slack.
 2022-02-03 18:28:11 +00:00
Combiz Khozoie
731f86e7f1
Update imperial_mb.config 
Removed my contact details.  Users can request help on the nf-core slack.
 2022-02-03 18:27:49 +00:00
Combiz Khozoie
453080f282
Update imperial.config 
Removed my contact details.  Users can request help on the nf-core slack.
 2022-02-03 18:26:30 +00:00
James A. Fellows Yates
50aafc6410
Update eva.config 2022-02-03 17:03:10 +01:00
James A. Fellows Yates
e02196d6ad
Update eva.config 2022-02-03 17:02:34 +01:00
James A. Fellows Yates
0e41349324
Update eva.config 2022-02-03 17:01:54 +01:00
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
James Fellows Yates
2562a2f563 Remove virtual free 2022-02-02 08:06:00 +01:00
James A. Fellows Yates
8739aabbf0
Bump markduplicates by default 2022-02-02 08:00:13 +01:00
Austyn Trull
1c9e1bf8a1 Fixing syntax in cheaha profile 2022-01-28 14:18:57 -06:00
Lara Ianov
9c0d550222
max_memory increase to reflect largemem 2022-01-28 11:45:13 -06:00
Austyn Trull
06541411dd Initial commit of cheaha profile 2022-01-28 11:37:42 -06:00
Harshil Patel
9792226f5c
Update genomes.config 2022-01-27 12:45:41 +00:00
Praveen Raj S
5c1afd56bf
Added genome parameter 
Added genome parameter to the config file
 2022-01-20 22:25:31 +01:00
Harshil Patel
cd6b8e0f17 Add --nextclade_dataset params 2022-01-17 16:51:55 +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
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
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
87e4ece034
Add files via upload 2021-12-17 00:36:51 -05:00
Venkat Malladi
306c802b4e
Fix name of Params 2021-12-16 09:27:23 -06:00
PCQ
698555f801
Rename marvin.conf to marvin.config 2021-12-15 14:44:05 +01:00
praveenraj2018
0557f4e062
Renamed star_index directory 2021-12-14 21:15:12 +01:00
Maxime U. Garcia
5e92e2ef11
Update conf/pipeline/rnavar/munin.config 2021-12-14 16:10:31 +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