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Merge pull request #422 from giusmar/master

Add TIGEM config file
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Alexander Peltzer 2022-10-05 16:40:24 +02:00 committed by GitHub
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5 changed files with 24 additions and 0 deletions

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@ -88,6 +88,7 @@ jobs:
- "sanger" - "sanger"
- "sbc_sharc" - "sbc_sharc"
- "seg_globe" - "seg_globe"
- "tigem"
- "uct_hpc" - "uct_hpc"
- "unibe_ibu" - "unibe_ibu"
- "uppmax" - "uppmax"

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@ -142,6 +142,7 @@ Currently documentation is available for the following systems:
- [SANGER](docs/sanger.md) - [SANGER](docs/sanger.md)
- [SBC_SHARC](docs/sbc_sharc.md) - [SBC_SHARC](docs/sbc_sharc.md)
- [SEG_GLOBE](docs/seg_globe.md) - [SEG_GLOBE](docs/seg_globe.md)
- [TIGEM](docs/tigem.md)
- [UCT_HPC](docs/uct_hpc.md) - [UCT_HPC](docs/uct_hpc.md)
- [UNIBE_IBU](docs/unibe_ibu.md) - [UNIBE_IBU](docs/unibe_ibu.md)
- [UPPMAX](docs/uppmax.md) - [UPPMAX](docs/uppmax.md)

14
conf/tigem.config Normal file
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@ -0,0 +1,14 @@
params {
config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.'
config_profile_contact = 'Giuseppe Martone (@giusmar)'
config_profile_url = 'https://github.com/giusmar'
}
process.executor = 'slurm'
google.zone = 'europe-west1'
singularity {
enabled = true
autoMounts = true
cacheDir = 'work/singularity'
}

7
docs/tigem.md Normal file
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@ -0,0 +1,7 @@
# nf-core/configs: TIGEM configuration
To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster.
---
This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.

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@ -70,6 +70,7 @@ profiles {
sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
sbc_sharc { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"} sbc_sharc { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"}
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
tigem { includeConfig "${params.custom_config_base}/conf/tigem.config"}
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" } unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }