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1757 commits 4 branches 0 tags 1.9 MiB
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290 commits

Author SHA1 Message Date
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
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
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 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
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
Emil
8453f6b41a Moves qualimap arg to pipeline-specific config 2022-05-30 12:58:12 +02:00
sofstam
54b3cda34d Add review suggestion 2022-05-12 11:00:26 +02:00
sofstam
c59149d64c Update docs for hasta config 2022-05-12 10:47:03 +02:00
James Fellows Yates
e1f780d976 Add taxprofiler for eVA 2022-05-12 07:54:17 +01:00
sofstam
5bc6ed90bd Add hasta config for taxprofiler 2022-05-11 11:13:31 +02:00
Thiseas C. Lamnidis
d09f5fc116
Update eva.config 
eigenstrat_snp_coverage also loads pandas
 2022-05-06 15:12:04 +02:00
Thiseas C. Lamnidis
209601f782
missing bracket 2022-05-04 13:08:13 +02:00
Thiseas C. Lamnidis
a42c4344ad
Exclude bionode 06 for software versions 2022-05-03 18:30:42 +02:00
Thiseas C. Lamnidis
79e227aa4e
Update eva.config 2022-05-03 16:42:21 +02:00
Thiseas C. Lamnidis
085726d081
Update eva.config 2022-05-03 16:36:05 +02:00
Thiseas C. Lamnidis
4592969613
memory for get_software_versions in MB. 2022-05-03 16:30:04 +02:00
Thiseas C. Lamnidis
79ad571319
Update eva.config 2022-05-03 16:25:48 +02:00
Thiseas C. Lamnidis
04226692fe
Update eva.config 2022-05-03 16:21:35 +02:00
Thiseas C. Lamnidis
57095fe79f
Update eva.config 
Set max heap size for java jobs in `get_software_versions`.
Limited OpenBLAS threading for python jobs that use numpy/pandas.
 2022-05-03 16:12:20 +02:00
James A. Fellows Yates
b5d9b79377
Merge branch 'nf-core:master' into master 2022-05-02 13:59:18 +02:00