millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 00:26:03 +00:00
Code Issues Releases Packages Activity

edit config and readme

Browse source
This commit is contained in:
ikeller 2021-05-19 09:46:07 +02:00
parent fb3cede5d3
commit af1e57027d
5 changed files with 34 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
.github/workflows/main.yml vendored
View file

@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles
strategy:
matrix:
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'unibe_ibu', 'uppmax', 'utd_ganymede', 'uzh']
steps:
- uses: actions/checkout@v1
- name: Install Nextflow

1
README.md
View file

@ -128,6 +128,7 @@ Currently documentation is available for the following systems:
* [SEG_GLOBE](docs/seg_globe.md)
* [SHH](docs/shh.md)
* [UCT_HPC](docs/uct_hpc.md)
* [UNIBE_IBU](docs/unibe_ibu.md)
* [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UZH](docs/uzh.md)

23
conf/unibe_ibu.config
View file

@ -0,0 +1,23 @@
params {
config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch"
config_profile_url = "https://www.bioinformatics.unibe.ch/"
max_memory = 500.GB
max_cpus = 128
max_time = 28.d
}
process {
executor = "slurm"
maxRetries = 2
beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/'
}
executor {
queueSize = 30
}
singularity {
enable = true
autoMounts = true
}

8
docs/unibe_ibu.md Normal file
View file

@ -0,0 +1,8 @@
# nf-core/configs: UNIBE_IBU Configuration
Configuration file to run nf-core pipelines on the cluster of the [Interfaculty Bioinformatics Unit](https://www.bioinformatics.unibe.ch/) of the University of Bern.
To use, run the pipeline with `-profile unibe_ibu`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.

1
nfcore_custom.config
View file

@ -47,6 +47,7 @@ profiles {
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }