109 commits

Author	SHA1	Message	Date
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
ameyner2	da8cf2f207	Added pipeline-specific config files for rnaseq and sarek	2021-03-24 10:46:26 +00:00
drpatelh	01a4f8559e	Update links to be consistent	2021-02-16 13:17:16 +00:00
Harshil Patel	6ffaf922c5	Update genomes.config	2021-02-16 10:28:32 +00:00
Harshil Patel	4de0855218	Update genomes.config	2021-02-15 18:48:03 +00:00
drpatelh	9d500cf679	Reorder params	2021-02-15 17:02:26 +00:00
drpatelh	f283dfb2dc	Add ARTIC primer sets to genome config	2021-02-15 16:58:30 +00:00
James A. Fellows Yates	86566ddd3b	Merge pull request #204 from jfy133/master ... Add a 'big_data' profile for eager @ SHH	2021-02-04 15:07:52 +01:00
James A. Fellows Yates	e32f1e46ff	Update shh.config	2021-02-04 08:13:16 +01:00
James A. Fellows Yates	c515a401c7	Update shh.config	2021-02-04 08:06:35 +01:00
James A. Fellows Yates	82fe8a04be	Update shh.config	2021-02-04 08:02:33 +01:00
James A. Fellows Yates	e7ac0bae13	Update shh.config	2021-02-04 08:00:57 +01:00
James A. Fellows Yates	eb725f9ea3	Update shh.config	2021-02-03 20:13:09 +01:00
James A. Fellows Yates	1c25cb033b	Add big_data profile	2021-01-19 13:53:01 +01:00
James A. Fellows Yates	a4c55b3ea9	Fix time limit 0-9 typo	2021-01-06 10:44:12 +01:00
Combiz Khozoie	a61992d144	Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO	2020-12-18 10:21:26 +00:00
Emelie Nilsso	febf38dd8e	Removed an old process so that only relevant processes are included	2020-11-26 13:38:47 +01:00
Emelie Nilsso	d61ed01d2d	Updated process names according to ampliseq main.nf	2020-11-25 17:50:30 +01:00
Emelie Nilsso	37e7cfae2c	Removed unnecessary code that was used to troubleshoot	2020-11-24 07:14:23 +01:00
Emelie Nilsso	2ea06ffab8	Modified uppmax and ampliseq specific config to fit with the divided preparation of the database	2020-11-23 21:20:36 +01:00
James A. Fellows Yates	804f53c58c	Merge pull request #178 from jfy133/master ... Add Max Planck Computing and Data Facility Cobra/Raven Clusters	2020-10-22 13:34:11 +02:00
MaxUlysse	8c0cc4b9ec	code polishing	2020-09-25 09:57:50 +02:00
MaxUlysse	81f910cc95	add specific BamQC config	2020-09-25 09:49:43 +02:00
MaxUlysse	fbe7bd133a	update uppmax specific sarek config	2020-09-25 08:33:53 +02:00
James A. Fellows Yates	11f1fb71db	Update mpcdf.config	2020-09-16 10:21:58 +02:00
James A. Fellows Yates	c6f7573d01	Update mpcdf.config	2020-09-15 17:48:54 +02:00
James A. Fellows Yates	bf87ec24e7	Update mpcdf.config	2020-09-15 17:45:38 +02:00
James A. Fellows Yates	3b7902d11b	Mad multi-core increase CPUs on retry	2020-09-06 08:23:35 +02:00
James A. Fellows Yates	4335e5deb7	Update mpcdf.config	2020-09-04 20:17:09 +02:00
James A. Fellows Yates	b4e275c3b9	Add MPCDF for EAGER	2020-09-04 19:57:25 +02:00
James A. Fellows Yates	5c7ab234b6	Create mpcdf.config	2020-09-04 19:55:40 +02:00
James A. Fellows Yates	c3fa87e4bc	Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH	2020-08-11 09:18:36 +02:00
James A. Fellows Yates	57ac9257a9	Remove now deprecated EAGER flag for HOPS profile	2020-07-20 11:29:12 +02:00
James A. Fellows Yates	84e03b8264	Re-bump default walltimes after debugging/testing	2020-07-11 18:31:04 +02:00
James A. Fellows Yates	8f6409d144	Remove min support percent value to avoid confusion	2020-07-08 15:26:19 +02:00
James A. Fellows Yates	1af9ce293c	Update hops profile based on requests from pathogen group	2020-07-08 15:22:33 +02:00
James A. Fellows Yates	c57a404f18	Add desc for hops	2020-07-08 10:45:43 +02:00
jfy133	15dad7e2e7	Add caveats for EAGER @ SHH profiles	2020-07-08 09:47:03 +02:00
jfy133	926c14f7ee	Cleverer process time submission	2020-07-08 09:36:56 +02:00
jfy133	563c27e1bb	Try again to get better time resource submission	2020-07-08 09:36:28 +02:00
James A. Fellows Yates	c6905b609e	Update shh.config	2020-07-08 09:25:21 +02:00
James A. Fellows Yates	b360ce26bc	Update shh.config	2020-07-08 09:24:06 +02:00
James A. Fellows Yates	31edb4b5d7	Update shh.config	2020-07-08 09:20:00 +02:00
James A. Fellows Yates	aac3478e86	Add better task time values to account for large data	2020-07-08 09:12:11 +02:00
James A. Fellows Yates	737d826932	Update shh.config	2020-07-08 08:36:04 +02:00
James A. Fellows Yates	fcdbeaa446	Merge branch 'master' into master	2020-07-07 14:34:10 +02:00
James A. Fellows Yates	af01fccba1	Add a HOPS profile for nf-core/eager @ SHH	2020-07-07 14:31:11 +02:00
James A. Fellows Yates	5517d2cbe0	Remove default non-profile bwa parameters from eager profile ... I realised today this is dangerous as these would not necessarily be reported if a user doesn't understand the profiles. Therefore removing these so nf-core/eager defaults are always used unless a specific profile (which would be described in the command itself) is explicitly named.	2020-07-07 13:29:13 +02:00
James A. Fellows Yates	530da4d8c0	Merge pull request #167 from jfy133/master ... Bump number of eager @shh retries to account for deep sequencing data	2020-06-30 11:33:29 +02:00