phue
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60ae267e43
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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
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2021-04-06 11:35:01 +02:00 |
|
ameynert
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6e201a71f4
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ATAC-seq pipeline config
Java processes with overhead memory requirements
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2021-03-30 16:31:00 +01:00 |
|
ameynert
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e5f2a63079
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Java overhead processes list updated
Added all processes calling GATK for Mutect2 variant calling
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2021-03-30 16:21:53 +01:00 |
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ameynert
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adfb5366b9
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Java overhead process list updated
Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
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2021-03-30 16:15:17 +01:00 |
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ameynert
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700776f759
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Change to shared Singularity cache
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2021-03-30 16:11:15 +01:00 |
|
ameynert
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25716fe849
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Merge pull request #2 from nf-core/master
Merge commits from nf-core/configs master
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2021-03-30 16:09:32 +01:00 |
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phue
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7c5a0871a3
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add note about required nextflow version
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2021-03-29 19:36:49 +02:00 |
|
phue
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8fc60e2e70
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add config for biohpc_gen
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2021-03-29 19:25:58 +02:00 |
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Gisela Gabernet
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71a97ba316
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Merge pull request #185 from ggabernet/master
awsbatch config update
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2021-03-28 20:59:40 +02:00 |
|
Phil Ewels
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d34bc40841
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UPPMAX: add to schema_ignore_params
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2021-03-26 15:22:57 +01:00 |
|
Phil Ewels
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eccc9ea8d5
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Define params.project and params.clusterOptions in uppmax config
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2021-03-26 15:20:32 +01:00 |
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Santiago Lacalle
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e2c583d558
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Remove "/rdsgpfs"
"/rdsgpfs" symlink will not be present on all nodes. Without that mount the container creation will fail.
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2021-03-25 12:38:15 +00:00 |
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Alexander Peltzer
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26b5904df1
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Merge pull request #218 from asafpr/master
added jax singularity cache dir
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2021-03-24 17:39:03 +01:00 |
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Asaf Peer
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922ab87eb0
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added jax singularity cache dir
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2021-03-24 11:25:47 -04:00 |
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ameynert
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6215414ecf
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Merge pull request #217 from ameynert/master
Addition of eddie institutional profile
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2021-03-24 14:05:07 +00:00 |
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ameynert
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3a8e54f153
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Removed sneaky trailing whitespace.
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2021-03-24 13:58:10 +00:00 |
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ameynert
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a0d42f5153
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Fixed code blocks for markdown linting
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2021-03-24 13:55:31 +00:00 |
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ameynert
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2d90c919aa
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Added eddie profile to github workflow tests
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2021-03-24 13:51:37 +00:00 |
|
Phil Ewels
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8e6223d1bd
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Update nfcore_custom.config
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2021-03-24 12:36:50 +01:00 |
|
Phil Ewels
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bfab371c94
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Merge branch 'master' into master
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2021-03-24 12:36:15 +01:00 |
|
Phil Ewels
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158402eddf
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Update nfcore_custom.config
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2021-03-24 12:26:49 +01:00 |
|
ameynert
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aeb0ffcfde
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Spacing fix
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
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2021-03-24 11:26:09 +00:00 |
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ameynert
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2a8ae2b214
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Update eddie.md
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2021-03-24 11:12:41 +00:00 |
|
ameynert
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96fe6185a0
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IGMM-specific docs
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2021-03-24 11:01:41 +00:00 |
|
ameyner2
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00d984d918
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Merge branch 'master' of github.com:ameynert/configs
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2021-03-24 10:46:43 +00:00 |
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ameyner2
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da8cf2f207
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Added pipeline-specific config files for rnaseq and sarek
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2021-03-24 10:46:26 +00:00 |
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Asaf Peer
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9b2d5bfead
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Merge pull request #216 from asafpr/master
Added JAX conf
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2021-03-24 03:31:14 -04:00 |
|
ameynert
|
791f3c95f3
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Pipeline specific configs moving to confs/pipeline
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2021-03-23 16:07:07 +00:00 |
|
Alexander Peltzer
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5988c51361
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Merge pull request #211 from DoaneAS/master
Adding WCM.config for Weill Cornell Medicine cluster
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2021-03-23 14:58:27 +01:00 |
|
Phil Ewels
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a9aae577ef
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Merge pull request #215 from Emiller88/ganymede-update
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2021-03-22 19:18:02 +01:00 |
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Edmund Miller
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a6975cdd4e
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fix(ganymede): large => high
Co-authored-by: drpatelh <drpatelh@users.noreply.github.com>
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2021-03-22 12:42:56 -05:00 |
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Edmund Miller
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34ccce9531
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fix(ganymede): Add process resources
Trimgalore though it can be a bottom neck, doesn't require the 1 big
memory node we have and can be run on the genomics queue.
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2021-03-21 21:47:59 -05:00 |
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Edmund Miller
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4570718b12
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fix(ganymede): Add TMPDIR and SINGULARITY_CACHEDIR env variables
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2021-03-21 21:45:39 -05:00 |
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Asaf Peer
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30c864e112
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added JAX conf
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2021-03-21 06:49:11 -04:00 |
|
Asaf Peer
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93bde78faa
|
added JAX conf
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2021-03-21 06:47:52 -04:00 |
|
ameynert
|
b48136a62e
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Added pipeline-specific config files
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2021-03-18 12:55:03 +00:00 |
|
ameynert
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af6a6b1060
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Details on running on eddie
Removed Conda support, Singularity by default. Added login and screen session on wild west node options.
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2021-03-18 12:48:48 +00:00 |
|
ameyner2
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bb388fb88b
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Merge branch 'master' of github.com:ameynert/configs
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2021-03-18 12:32:11 +00:00 |
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ameyner2
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059d353a1e
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Removed Conda, added automount Singularity
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2021-03-18 12:31:56 +00:00 |
|
Rike
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6221b67bcf
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Give Strelka a complete compute node
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2021-03-18 11:11:02 +01:00 |
|
Rike
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b1846af9d3
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reduce mapping resource further to compute node
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2021-03-18 11:10:00 +01:00 |
|
FriederikeHanssen
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67c93a4743
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Update conf/pipeline/sarek/cfc.config
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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2021-03-18 11:06:38 +01:00 |
|
ameynert
|
4ad6bb2bec
|
Singularity info
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2021-03-17 14:50:40 +00:00 |
|
Rike
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b70097e495
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remove new line
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2021-03-17 15:46:18 +01:00 |
|
Harshil Patel
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2ce1e2a9cc
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Create rnaseq.config
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2021-03-17 12:32:47 +00:00 |
|
ameyner2
|
d4cd07c646
|
Typo in beforescript
|
2021-03-17 09:21:26 +00:00 |
|
Maxime Garcia
|
ec11a9a951
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Merge pull request #212 from noirot/master
Add IFB config
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2021-03-16 16:55:38 +01:00 |
|
Noirot Céline
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e3216ccf79
|
typo
|
2021-03-16 16:00:56 +01:00 |
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Noirot Céline
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cc17045914
|
Add institution
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2021-03-16 15:58:29 +01:00 |
|
Noirot Céline
|
7e9f83ee81
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Add IFB config
|
2021-03-16 15:54:19 +01:00 |
|