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413 commits

Author SHA1 Message Date
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
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
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
Gwennid
96fd2bf217 Fixed formatting 2022-07-06 11:42:05 +02:00
Gwenna Breton
1d13dd9fbc
Changed where cgg-it is mentioned 2022-07-06 11:24:03 +02:00
Gwenna Breton
235097e58e
Addressed review comments
- removed mention of iGenomes
- clarified whom to contact for support
2022-07-06 11:20:59 +02:00
Gwenna Breton
1d7a34b11f
Removed comment about internal doc 2022-07-06 11:17:58 +02:00
Gwenna Breton
b202ad70ac
Removed mention of specific module versions 2022-07-06 11:16:38 +02:00
Gwenna Breton
84174043e4
Added details for nf-core pipelines download 2022-06-30 16:41:50 +02:00
Gwenna Breton
2398110ea5
Added info on dowloading pipelines 2022-06-30 14:24:17 +02:00
Gwenna Breton
22f73b06f9 Updated info about the different profiles 2022-06-30 12:00:05 +02:00
Gwenna Breton
f718025e79 Added doc file for medair 2022-06-30 11:43:04 +02:00
Bruno Grande
6f0d9e6c43 Complete check_max() move to global config 2022-06-23 10:10:28 -07:00
Bruno Grande
1c7230cb08 Add Sage-specific Sarek config 2022-06-23 09:15:42 -07:00
Bruno Grande
2898736cbe Add Sage Bionetworks nf-core configuration 2022-06-08 14:16:52 -07:00
Åshild J. Vågene
34feaa8b6b
prettier output 2022-06-03 17:08:15 +02:00
Åshild J. Vågene
2d82218318
typo 2022-06-03 16:42:08 +02:00
Åshild J. Vågene
144ca851c1
Update mjolnir_globe.md 2022-06-03 15:36:19 +02:00
Phil Ewels
b51059a3ae
Merge branch 'master' into config_ucph-mjolnir_ash 2022-06-03 13:21:36 +02:00
James A. Fellows Yates
7353fb257d
Merge pull request #380 from jfy133/taxprofiler
Add MAG @ EVA profile
2022-06-03 12:54:47 +02:00
James A. Fellows Yates
97d57539e3
Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-03 12:51:20 +02:00