millironx/nf-configs
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1843 commits 4 branches 0 tags 1.9 MiB
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306 commits

Author SHA1 Message Date
ameynert
70e3eafeb1
Merge pull request #6 from nf-core/master 
Merge base repository into fork
 2022-10-26 16:25:37 +02:00
Athanasios Baltzis
7547fba92e Add proteinfold-specific CRG config 2022-10-20 18:00:14 +02:00
Alexander Peltzer
c2710b1b63
Merge branch 'master' into varskip_designs 2022-10-19 10:42:00 +02:00
Edmund Miller
0cabf67b61
feat(demultiplex): Add optimized transfers for bases2fastq 2022-10-05 17:21:23 -05:00
Lewis Quayle
755862fc61
Merge branch 'nf-core:master' into sbc_sharc 2022-10-05 19:55:43 +01:00
Alexander Peltzer
8b68ffce89
Merge branch 'master' into custom-mag-eva 2022-10-04 21:55:37 +02:00
lquayle88
584052cfff Revised base and all pipeline configs to provide memory on per core basis 2022-10-04 09:12:29 +01:00
lquayle88
3f2ffa314d Revised base and sarek configs to provide memory on per core basis 2022-10-04 00:25:16 +01:00
lquayle88
e7ac3ecd19 Modified resource requests in sbc_sharc.config for sarek 2022-10-02 00:24:39 +01:00
lquayle88
9b451b53b7 Increased cpus and memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek 2022-10-01 23:31:51 +01:00
lquayle88
10c1490265 Increased memory and time for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek 2022-10-01 23:15:13 +01:00
lquayle88
dbb3b3b44b Reinstated maxRetries and increased memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek 2022-10-01 07:45:28 +01:00
lquayle88
8103718389 Reduced maxRetries upon error in sbc_sharc.config for sarek 2022-09-30 16:54:48 +01:00
lquayle88
c42a5a9a94 Updated resources requested by pipelines 2022-09-23 17:01:58 +01:00
lquayle88
ab1ad832df Updated resource requests for compatibility with high memory nodes 2022-09-23 13:18:50 +01:00
lquayle88
7e34beb3c9 Updated resource requests for compatibility with general worker nodes 2022-09-23 11:08:39 +01:00
lquayle88
55971bb94d Modularised error handling strategy to per pipeline basis 2022-09-16 17:29:08 +01:00
ameynert
9167e81214
Added other Java processes with memory overhead, sorted alphabetically 2022-09-14 09:07:09 +01:00
lquayle88
9fef35d7d3 Updated pipeline configs for atacseq and chipseq 2022-09-13 17:08:56 +01:00
lquayle88
a9b62c53e0 Added global institutional and pipeline configs for sbc_sharc 2022-09-13 17:02:44 +01:00
ameynert
91ef9a3241
Added another Java process with overhead 2022-09-13 09:27:13 +01:00
ameynert
a808933da8
Added another Java process that needs memory overhead 2022-09-09 08:37:21 +01:00
ameynert
29a0b30d85
Updated process names to Sarek 3 2022-09-07 16:00:52 +01:00
Simon Pearce
2c738cae33
Update crukmi.config 2022-09-01 11:24:11 +01:00
Simon Pearce
a8faeda141
Update crukmi.config 2022-09-01 11:23:07 +01:00
SPearce
800931bff2 Add Sarek specific config 2022-09-01 11:13:23 +01:00
Annick Renevey
51871ea6fc rnafusion setup for hasta usage 2022-08-31 11:32:01 +02:00
Harshil Patel
8b9661825b Replace NC_063383.1 fasta and gff and add Nextclade config 2022-08-24 15:21:44 +01:00
Harshil Patel
8dcfcfd856 Add monkeypox genome files to viralrecon genome config file 2022-08-24 12:13:17 +01:00
Ramprasad Neethiraj
9182b55acc
Merge branch 'master' into feat/hasta_update 2022-08-23 11:21:58 +02:00
Ramprasad Neethiraj
7ff2977a29 Merge branch 'master' of github.com:nf-core/configs into feat/hasta_update 2022-08-18 15:58:56 +02:00
Ramprasad Neethiraj
dd63dee7aa update conf 2022-08-18 15:56:41 +02:00
Ramprasad Neethiraj
1c942759ea update sentieon 2022-08-18 15:52:31 +02:00
Ramprasad Neethiraj
a6cce4ab6a
Merge branch 'master' into feat/hasta_java_memory_fix 2022-08-18 13:36:08 +02:00
Harshil Patel
2ab126fa4d
Update default Nextclade dataset to 2022-06-14T12:00:00Z 2022-07-11 18:28:41 +01:00
James A. Fellows Yates
51d057564f
Fix python related seg faults mag@eva 2022-06-15 15:40:42 +02:00
James Fellows Yates
acabcbd9e8 Use _JAVA_OPTIONS instead 2022-06-15 15:27:40 +02:00
James Fellows Yates
76b0d1dd85 Merge branch 'eva-java-correction' of github.com:jfy133/nf-core-configs into eva-java-correction 2022-06-15 15:22:25 +02:00
James Fellows Yates
58dd9d49c7 Move beforeScript exports to env scope 2022-06-15 15:21:20 +02:00
Emil Bertilsson
c8c795595a
Merge branch 'nf-core:master' into feat/hasta_java_memory_fix 2022-06-09 15:10:46 +02:00
Emil Bertilsson
72e995f326 Adds generic fix for java memory issue on slurm 2022-06-09 10:28:20 +02:00
Maxime U. Garcia
c08cb5e97e
Merge branch 'master' into varskip_designs 2022-06-07 11:58:49 +02:00
James A. Fellows Yates
46fba9c597
Update eva.config 2022-06-03 21:10:48 +02:00
James A. Fellows Yates
05cc8a08f1
Update eva.config 2022-06-03 21:08:19 +02:00
James Fellows Yates
9ef52af084 Increase overhead 2022-06-03 14:24:27 +02:00
James Fellows Yates
c40ebb9acf Add overhead for get_software_versions 2022-06-03 14:21:41 +02:00
James Fellows Yates
df0429ce9d Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS 2022-06-03 14:20:39 +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 Fellows Yates
5a67eba04c Add MAG @ EVA profile 2022-06-03 12:41:08 +02:00
Emil Bertilsson
80e2a50a2f
Merge pull request #378 from raysloks/feat/hasta_java_memory_fix 
Feat/hasta java memory fix
 2022-05-30 14:40:52 +02:00