mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 16:29:55 +00:00
James A. Fellows Yates
GitHub
commit
5d8c4f9c50
11 changed files with 563 additions and 17 deletions
2
.github/workflows/main.yml
vendored
2
.github/workflows/main.yml
vendored
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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needs: test_all_profiles
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strategy:
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strategy:
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matrix:
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matrix:
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profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
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profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
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steps:
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steps:
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- uses: actions/checkout@v1
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- uses: actions/checkout@v1
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- name: Install Nextflow
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- name: Install Nextflow
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24
README.md
24
README.md
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@ -4,9 +4,8 @@
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A repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different Institutions.
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A repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different Institutions.
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## Table of contents
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## Table of contents <!-- omit in toc -->
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* [Table of contents](#table-of-contents)
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* [Using an existing config](#using-an-existing-config)
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* [Using an existing config](#using-an-existing-config)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Offline usage](#offline-usage)
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@ -14,11 +13,11 @@ A repository for hosting Nextflow configuration files containing custom paramete
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* [Checking user hostnames](#checking-user-hostnames)
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* [Checking user hostnames](#checking-user-hostnames)
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* [Testing](#testing)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Documentation](#documentation)
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* [Uploading to nf-core/configs](#uploading-to-nf-coreconfigs)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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* [Pipeline-specific documentation](#pipeline-specific-documentation)
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* [Pipeline-specific documentation](#pipeline-specific-documentation)
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* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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* [Create the pipeline-specific nf-core/configs files](#create-the-pipeline-specific-nf-coreconfigs-files)
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* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
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* [Help](#help)
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* [Help](#help)
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## Using an existing config
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## Using an existing config
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@ -99,7 +98,8 @@ Currently documentation is available for the following systems:
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* [BINAC](docs/binac.md)
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* [BINAC](docs/binac.md)
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* [CBE](docs/cbe.md)
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* [CBE](docs/cbe.md)
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* [CCGA](docs/ccga.md)
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* [CCGA](docs/ccga.md)
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* [CCGA_DX](/docs/ccga_dx.md)
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* [CCGA_DX](docs/ccga_dx.md)
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* [CCGA_MED](docs/ccga_med.md)
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* [CFC](docs/binac.md)
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* [CFC](docs/binac.md)
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* [CRICK](docs/crick.md)
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* [CRICK](docs/crick.md)
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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@ -126,7 +126,14 @@ Within the local clone of your fork add the custom config file to the [`conf/`](
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You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
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You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
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You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
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You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone.
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Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that.
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In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error:
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```bash
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Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
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Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.
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set(['<profile_name>'])
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##[error]Process completed with exit code 1.
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```
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
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@ -156,10 +163,11 @@ Currently documentation is available for the following pipeline within the speci
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* ampliseq
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* ampliseq
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* [BINAC](docs/pipeline/ampliseq/binac.md)
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* [BINAC](docs/pipeline/ampliseq/binac.md)
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* eager
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* eager
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* [SHH](docs/pipeline/eager/shh.md)
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* [SHH](docs/pipeline/eager/shh.md)
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* [UPPMAX](docs/pipeline/sarek/uppmax.md)
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### Enabling pipeline-specific configs within a pipeline
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### Enabling pipeline-specific configs within a pipeline
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|
||||||
|
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|
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|
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|
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|
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|
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|
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|
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|
class="st7" />
|
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|
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|
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|
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|
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|
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|
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|
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|
</svg>
|
||||||
|
After Width: | Height: | Size: 26 KiB |
|
|
@ -13,15 +13,14 @@ singularity {
|
||||||
process {
|
process {
|
||||||
beforeScript = 'module load devel/singularity/3.4.2'
|
beforeScript = 'module load devel/singularity/3.4.2'
|
||||||
executor = 'pbs'
|
executor = 'pbs'
|
||||||
queue = 'short'
|
queue = { task.memory >= 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time > 48.h ? 'long' : 'short'}
|
||||||
process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'short' : 'long'}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
params {
|
params {
|
||||||
igenomes_base = '/nfsmounts/igenomes'
|
igenomes_base = '/nfsmounts/igenomes'
|
||||||
max_memory = 1000.GB
|
max_memory = 1000.GB
|
||||||
max_cpus = 28
|
max_cpus = 28
|
||||||
max_time = 48.h
|
max_time = 168.h
|
||||||
}
|
}
|
||||||
|
|
||||||
weblog{
|
weblog{
|
||||||
|
|
|
||||||
39
conf/ccga_med.config
Normal file
39
conf/ccga_med.config
Normal file
|
|
@ -0,0 +1,39 @@
|
||||||
|
//Profile config names for nf-core/configs
|
||||||
|
params {
|
||||||
|
config_profile_description = 'CCGA Med cluster profile provided by nf-core/configs.'
|
||||||
|
config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
|
||||||
|
config_profile_url = 'https://www.ccga.uni-kiel.de/'
|
||||||
|
}
|
||||||
|
|
||||||
|
/*
|
||||||
|
* -------------------------------------------------
|
||||||
|
* Nextflow config file for CCGA cluster in Kiel
|
||||||
|
* -------------------------------------------------
|
||||||
|
*/
|
||||||
|
|
||||||
|
singularity {
|
||||||
|
enabled = true
|
||||||
|
runOptions = "-B /work_ifs -B /scratch"
|
||||||
|
cacheDir = "/work_ifs/ikmb_repository/singularity_cache/"
|
||||||
|
}
|
||||||
|
|
||||||
|
executor {
|
||||||
|
queueSize=100
|
||||||
|
}
|
||||||
|
|
||||||
|
process {
|
||||||
|
|
||||||
|
// Global process config
|
||||||
|
executor = 'slurm'
|
||||||
|
queue = 'all'
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
params {
|
||||||
|
// illumina iGenomes reference file paths on RZCluster
|
||||||
|
igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/'
|
||||||
|
saveReference = true
|
||||||
|
max_memory = 250.GB
|
||||||
|
max_cpus = 24
|
||||||
|
max_time = 120.h
|
||||||
|
}
|
||||||
17
conf/pipeline/sarek/uppmax.config
Normal file
17
conf/pipeline/sarek/uppmax.config
Normal file
|
|
@ -0,0 +1,17 @@
|
||||||
|
// sarek/uppmax specific profile config
|
||||||
|
|
||||||
|
params {
|
||||||
|
config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
|
||||||
|
config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs'
|
||||||
|
|
||||||
|
singleCPUmem = 7000.MB
|
||||||
|
// Just useful until iGenomes is updated on UPPMAX
|
||||||
|
igenomeIgnore = true
|
||||||
|
genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle'
|
||||||
|
}
|
||||||
|
if (hostname ==~ "r.*") {
|
||||||
|
params.singleCPUmem = 6400.MB
|
||||||
|
}
|
||||||
|
if (hostname ==~ "i.*") {
|
||||||
|
params.singleCPUmem = 15.GB
|
||||||
|
}
|
||||||
16
docs/ccga_med.md
Normal file
16
docs/ccga_med.md
Normal file
|
|
@ -0,0 +1,16 @@
|
||||||
|
# nf-core/configs: CCGA Med Cluster Configuration
|
||||||
|
|
||||||
|
Deployment and testing of nf-core pipelines at the CCGA Med cluster is on-going.
|
||||||
|
|
||||||
|
To use, run the pipeline with `-profile ccga_med`. This will download and launch the [`ccga_med.config`](../conf/ccga_med.config) which has been pre-configured with a setup suitable for the CCGA 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.
|
||||||
|
|
||||||
|
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:
|
||||||
|
|
||||||
|
```bash
|
||||||
|
## Load Nextflow and Singularity environment modules
|
||||||
|
module purge
|
||||||
|
module load nextflow
|
||||||
|
module load singularity
|
||||||
|
```
|
||||||
|
|
||||||
|
>NB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner).
|
||||||
18
docs/pipeline/sarek/uppmax.md
Normal file
18
docs/pipeline/sarek/uppmax.md
Normal file
|
|
@ -0,0 +1,18 @@
|
||||||
|
# nf-core/configs: uppmax sarek specific configuration
|
||||||
|
|
||||||
|
Extra specific configuration for sarek pipeline
|
||||||
|
|
||||||
|
## Usage
|
||||||
|
|
||||||
|
To use, run the pipeline with `-profile uppmax`.
|
||||||
|
|
||||||
|
This will download and launch the sarek specific [`uppmax.config`](../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
|
||||||
|
|
||||||
|
Example: `nextflow run nf-core/sarek -profile uppmax`
|
||||||
|
|
||||||
|
## Sarek specific configurations for uppmax clusters
|
||||||
|
|
||||||
|
Specific configurations for uppmax clusters has been made for sarek.
|
||||||
|
|
||||||
|
* Set paths to reference genomes
|
||||||
|
* Set path to singularity containers for `irma`
|
||||||
|
|
@ -8,9 +8,6 @@
|
||||||
* name here.
|
* name here.
|
||||||
*/
|
*/
|
||||||
|
|
||||||
params.custom_config_version = 'master'
|
|
||||||
params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
|
|
||||||
|
|
||||||
//Please use a new line per include Config section to allow easier linting/parsing. Thank you.
|
//Please use a new line per include Config section to allow easier linting/parsing. Thank you.
|
||||||
profiles {
|
profiles {
|
||||||
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
|
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
|
||||||
|
|
@ -19,6 +16,7 @@ profiles {
|
||||||
cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
|
cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
|
||||||
ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
|
ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
|
||||||
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
|
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
|
||||||
|
ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
|
||||||
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
|
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
|
||||||
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
|
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
|
||||||
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
|
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
|
||||||
|
|
|
||||||
|
|
@ -10,4 +10,5 @@
|
||||||
|
|
||||||
profiles {
|
profiles {
|
||||||
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
|
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
|
||||||
|
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
|
||||||
}
|
}
|
||||||
Loading…
Reference in a new issue