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433 commits

Author SHA1 Message Date
Cedric Arisdakessian
32cdea4b59 documentation for mana config 2022-10-03 03:38:48 +00:00
Bruno Grande
735df9ef76
Merge branch 'master' into bgrande/sage-improve-downloads 2022-09-26 10:22:27 -07:00
Patrick Hüther
51ae760889
Merge pull request #413 from phue/biohpc_charliecloud_patch
biohpc_gen: update required modules
2022-09-25 23:28:04 +02:00
AdrijaK
798d845a0d run prettier 2022-09-22 14:21:02 +02:00
Adrija Kalvisa
7959b14385
Merge branch 'nf-core:master' into master 2022-09-22 13:15:32 +02:00
Patrick Hüther
85aa6adeed
Merge branch 'master' into biohpc_charliecloud_patch 2022-09-18 12:52:33 +02:00
Bruno Grande
8bb9361359 Improve reliability of file transfers 2022-09-17 10:14:04 -07:00
James A. Fellows Yates
ec638e62de
Apply suggestions from code review
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-09-15 09:10:29 +02:00
James Fellows Yates
c0effc0366 Add HKI profile files 2022-09-14 15:34:27 +02:00
lquayle88
be356eb400 Ran prettier on docs/sbc_sharc.md 2022-09-14 10:24:56 +01:00
lquayle88
32403b6222 Updated pipeline config docs for atacseq, chipseq and rnaseq 2022-09-14 08:46:11 +01:00
lquayle88
91bfa7341f Made changes requested for PR 2022-09-14 08:42:40 +01:00
Lewis Quayle
61ae463606
Updated sbc_sharc.md 2022-09-13 17:13:57 +01:00
lquayle88
a9b62c53e0 Added global institutional and pipeline configs for sbc_sharc 2022-09-13 17:02:44 +01:00
phue
b20f28a3c9 biohpc_gen: load charliecloud from lrz software tree and remove conda fallback
the biohpc_gen specific software tree is less maintained and outdated
2022-09-05 11:25:33 +02:00
Bruno Grande
80831358f9
Merge branch 'master' into bgrande/sage-aws 2022-09-01 13:21:36 -07:00
SPearce
a142ad7eae Added link to Sarek specific documentation 2022-09-01 13:55:08 +01:00
Simon Pearce
14a97ad0e8
Merge branch 'master' into crukmi 2022-09-01 10:07:24 +01:00
ameynert
28e59e38b4
Run prettier 2022-09-01 09:28:05 +01:00
Kalayanee Chairat
700f14d828
Merge pull request #1 from nf-core/master
Merging from master
2022-09-01 15:07:43 +07:00
Simon Pearce
864da0b5be
Merge branch 'master' into crukmi 2022-08-31 18:19:47 +01:00
Bruno Grande
9a37404a04
Merge branch 'master' into bgrande/sage-aws 2022-08-31 09:22:07 -07:00
Bruno Grande
c883723559 Simplify resource adjustments 2022-08-31 09:10:30 -07:00
Annick Renevey
0851903f66 include new config in pipeline configs file 2022-08-31 14:19:07 +02:00
Austyn Trull
90f638d376 Updating the cheaha documentation to clarify that /data/temporary-scratch/atrull will be used as storage for files that would normally go into one of the temporary locations when using Singularity 2022-08-29 10:47:46 -05:00
Bruno Grande
9c8cb71bc7
Merge branch 'master' into bgrande/sage-aws 2022-08-25 16:29:20 -07:00
Bruno Grande
317e5a16cb Improve AWS-related config for Sage profile 2022-08-25 16:24:52 -07:00
kalayaneech
93c4ba67a0 adding adcra configuration 2022-08-25 16:17:09 +07:00
SPearce
d0662a3acb Ran prettier 2022-08-15 09:33:30 +01:00
SPearce
a97b887d93 Written a help file 2022-08-12 16:57:04 +01:00
SPearce
0bfedde296 Initial attempt at a CRUKMI config file 2022-08-12 15:43:22 +01:00
Gwenna Breton
0e4f2b40d3
Added email of IT group 2022-08-08 16:14:17 +02:00
Gwenna Breton
2740b5efbf
Update docs/medair.md
Fixed typo

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2022-08-08 16:08:05 +02:00
Gwenna Breton
648025c1ce
Clarified where to store singularity images 2022-08-08 16:04:21 +02:00
Gwenna Breton
6aa78833c3
Merge branch 'master' into medair 2022-08-01 16:46:55 +02:00
Matthieu Muffato
dda1d810b1 Latest stable version (rather than an edge one) 2022-07-20 14:35:39 +01:00
Matthieu Muffato
1ee20f0bb0 2 cores should be enough for the nextflow manager itself 2022-07-20 14:35:22 +01:00
Matthieu Muffato
60dc451569 The oversubscribed queue is recommended for workflow managers 2022-07-20 14:34:59 +01:00
Matthieu Muffato
1f1a9ac5f0 ISG provide the module, not the pathogen informatics team 2022-07-20 14:34:25 +01:00
Matthieu Muffato
2aad355fbf The config doesn't mandate Singularity any more (Conda is fine too) 2022-07-20 14:32:43 +01:00
Priyanka Surana
fd87fbcb9d Sanger profile update 2022-07-20 13:22:51 +01:00
qlr900
ff55ec67b4 update to current java+nextflow module combination 2022-07-07 14:30:48 +02:00
Gwenna Breton
6b9cdc8ef3
Added info about Sentieon singularities 2022-07-07 14:24:15 +02:00
Gwenna Breton
746db14d47
Update medair.md
- updated text about storing singularity images
- updated text about using profiles
2022-07-07 11:42:46 +02:00
qlr900
d19d6c0ae0 update wording 2022-07-06 16:19:16 +02:00
qlr900
4f98876429 add export to NXF_SINGULARITY_CACHEDIR 2022-07-06 13:35:10 +02:00
qlr900
f45b8645f6 update wording 2022-07-06 13:05:13 +02:00
qlr900
8a781b6bb2 modify alternative module load 2022-07-06 12:54:07 +02:00
qlr900
7ac08a1015 add alternative module load 2022-07-06 12:42:14 +02:00
Gwennid
96fd2bf217 Fixed formatting 2022-07-06 11:42:05 +02:00