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Author SHA1 Message Date
Anthony Underwood
3e8f9b3d4e
Remove blank lines 2021-04-22 15:57:09 +01:00
Anthony Underwood
f414446a88
Add info on how to load Singularity into your path 2021-04-22 15:38:36 +01:00
Anthony Underwood
b16b011bcc
Add ~/bin as recommended location for nextflow executable 2021-04-22 12:02:11 +01:00
Anthony Underwood
351c5773f0
Add queue limits for 'normal' 2021-04-22 11:59:34 +01:00
Anthony Underwood
fa267c0cf9
Add sanger to tests 2021-04-21 21:01:25 +01:00
Anthony Underwood
6175362049
Add sanger profile 2021-04-21 20:47:48 +01:00
Anthony Underwood
cc18d213dc
Update sanger.md 2021-04-21 20:24:08 +01:00
Anthony Underwood
40eb3e0201
Update sanger.md 2021-04-21 20:20:30 +01:00
Anthony Underwood
7163e8723d
Create sanger.md 2021-04-21 20:17:42 +01:00
Anthony Underwood
7d8770af1a
Create sanger.config 2021-04-21 16:39:55 +01:00
Maxime Garcia
7498e29ec0
Merge pull request #201 from maxulysse/master_uppmax_offline 
Improve offline docs for Bianca
 2021-04-21 13:04:15 +02:00
Maxime Garcia
1548690ca6
Update docs/uppmax.md 
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
 2021-04-21 12:27:27 +02:00
Patrick Hüther
fff04ce0ba
Merge pull request #233 from phue/biohpc_gen 
biohpc_gen: update software tree path
 2021-04-21 12:14:06 +02:00
MaxUlysse
bab9241243 fix: markdownlint 2021-04-21 11:51:14 +02:00
MaxUlysse
844246cc7d fix: clearer usage of module 2021-04-21 11:28:58 +02:00
MaxUlysse
1a7ec56c33 feat: more details 2021-04-21 11:23:50 +02:00
MaxUlysse
c89877decc feat: use <PIPLEINE> 2021-04-21 11:17:06 +02:00
MaxUlysse
658fa7ccda fix: markdownlint 2021-04-21 11:08:16 +02:00
Maxime Garcia
79e3dd65a7
Apply suggestions from code review 
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
 2021-04-21 11:06:39 +02:00
phue
b225a0555a biohpc_gen: update software tree path 2021-04-21 10:08:00 +02:00
Maxime Garcia
4eea06f0db
Apply suggestions from code review 
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
 2021-04-20 16:03:34 +02:00
MaxUlysse
1c1dd952fc fix: bullet list 2021-04-20 15:58:51 +02:00
Maxime Garcia
e4d2ef0984
Apply suggestions from code review 
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2021-04-20 15:53:54 +02:00
MaxUlysse
4930795cab feat: more complete docs 2021-04-20 15:38:49 +02:00
MaxUlysse
10abca712b fix: first draft of bianca guide 2021-04-16 17:01:58 +02:00
Alexander Peltzer
a525be112f
Merge pull request #232 from jfy133/update-mpcdf 
Update mpcdf to use singularity
 2021-04-16 09:28:46 +02:00
James A. Fellows Yates
12a4518803
Markdown lint fix 2021-04-15 22:29:15 +02:00
James A. Fellows Yates
b9a00f7926
Update mpcdf.config 2021-04-15 22:27:07 +02:00
James A. Fellows Yates
0fc90586e0
Update mpcdf.md 2021-04-15 22:26:37 +02:00
Harshil Patel
7ac66dcd72
Update crick.config 2021-04-13 17:07:02 +01:00
Combiz Khozoie
c571c05ab9
Merge pull request #219 from slacalle/patch-2 
Imperial College | Remove "/rdsgpfs"
 2021-04-13 15:28:00 +01:00
Phil Ewels
2f77d16b70
Merge pull request #220 from ewels/master 
UPPMAX: Avoid undefined parameter warnings
 2021-04-08 15:06:00 +02:00
James A. Fellows Yates
a2a47fdecc
Merge pull request #224 from jfy133/eva 
Add EVA profile for MPI-EVA (clean)
 2021-04-07 19:56:00 +02:00
James A. Fellows Yates
161c3a33d4
Merge branch 'master' into eva 2021-04-07 19:28:16 +02:00
James A. Fellows Yates
ce465cca57
Apply suggestions from code review 
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
 2021-04-07 19:27:24 +02:00
Alexander Peltzer
91f50aad4e
Merge pull request #221 from phue/biohpc_gen 
Add BioHPC Genomics config
 2021-04-07 14:03:22 +02:00
Patrick Hüther
53b54ba845
Remove whitespace 
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
 2021-04-07 13:18:06 +02:00
ameynert
efa051b3e4
Merge pull request #222 from ameynert/master 
Addition of ATAC-seq pipeline config, updated docs
 2021-04-07 09:48:29 +01:00
ameynert
0ab9edde72
Delete conf/pipeline/atacseq directory 
Pipeline-specific config not supported yet by ATAC-seq pipeline
 2021-04-07 09:24:30 +01:00
James Fellows Yates
8dac4ca552 Merge branch 'eva' of github.com:jfy133/configs into eva 2021-04-06 17:53:32 +02:00
James Fellows Yates
60c66d93ac Markdown linting 2021-04-06 17:53:27 +02:00
James A. Fellows Yates
832edaa450
Merge branch 'master' into eva 2021-04-06 17:51:46 +02:00
James A. Fellows Yates
504c10d6ff
Update README.md 2021-04-06 17:50:25 +02:00
James Fellows Yates
be1d35840d Add EVA and EAGER@EVA 2021-04-06 17:48:16 +02:00
James Fellows Yates
d69af0f287 Merging 2021-04-06 16:42:22 +02:00
phue
60ae267e43 use SLURM_CLUSTERS env var 
this seems to be more reliable for queue checking than using the clusterOptions directive. See https://github.com/nextflow-io/nextflow/issues/807
 2021-04-06 11:35:01 +02:00
ameynert
6e201a71f4
ATAC-seq pipeline config 
Java processes with overhead memory requirements
 2021-03-30 16:31:00 +01:00
ameynert
e5f2a63079
Java overhead processes list updated 
Added all processes calling GATK for Mutect2 variant calling
 2021-03-30 16:21:53 +01:00
ameynert
adfb5366b9
Java overhead process list updated 
Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
 2021-03-30 16:15:17 +01:00
ameynert
700776f759
Change to shared Singularity cache 2021-03-30 16:11:15 +01:00