mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-23 02:48:17 +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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strategy:
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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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- uses: actions/checkout@v1
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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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## 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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* [Configuration and parameters](#configuration-and-parameters)
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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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* [Testing](#testing)
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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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* [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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* [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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## 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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* [CBE](docs/cbe.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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* [CRICK](docs/crick.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 [`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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@ -156,10 +163,11 @@ Currently documentation is available for the following pipeline within the speci
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* ampliseq
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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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* [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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d="m 15.436598,-51.575821 q 3.090064,-1.663881 9.428657,-3.090064 6.338593,-1.426184 11.330235,-1.426184 8.477868,0 12.756419,3.327762 4.27855,3.327761 4.27855,10.934073 v 26.939021 h -11.80563 v -24.562049 q 0,-6.89322 -7.764776,-6.89322 -1.743113,0 -3.565459,0.396162 -1.822345,0.396162 -2.852367,0.950789 v 30.108318 H 15.436598 Z"
|
||||
style="font-weight:bold;font-size:79.23241425px;line-height:0%;font-family:'Maven Pro';fill:#24af63;fill-opacity:1;stroke:none;stroke-width:0.37753597"
|
||||
id="path559"
|
||||
inkscape:connector-curvature="0" />
|
||||
<path
|
||||
d="m 66.729683,-45.95032 h -5.863199 v -9.032495 h 5.942431 v -0.950789 q 0.07923,-9.032495 4.120086,-12.518721 4.120085,-3.565459 11.17177,-3.565459 1.267719,0 2.773134,0.237697 1.505416,0.237697 2.456205,0.554627 v 10.379446 q -0.871556,-0.871556 -1.743113,-1.267718 -0.871556,-0.475395 -2.218507,-0.475395 -2.218508,0 -3.486227,1.188486 -1.267718,1.188487 -1.267718,4.040854 v 2.376972 h 8.715565 v 9.032495 h -8.794798 v 31.059107 H 66.729683 Z"
|
||||
style="font-weight:bold;font-size:79.23241425px;line-height:0%;font-family:'Maven Pro';fill:#24af63;fill-opacity:1;stroke:none;stroke-width:0.37753597"
|
||||
id="path561"
|
||||
inkscape:connector-curvature="0" />
|
||||
<path
|
||||
d="m 96.008535,-43.256418 h 24.165885 v 8.160939 H 96.008535 Z"
|
||||
style="font-weight:bold;font-size:79.23241425px;line-height:0%;font-family:'Maven Pro';fill:#24af63;fill-opacity:1;stroke:none;stroke-width:0.37753597"
|
||||
id="path563"
|
||||
inkscape:connector-curvature="0" />
|
||||
<path
|
||||
style="display:inline;fill:url(#f);stroke-width:0.37753597"
|
||||
inkscape:connector-curvature="0"
|
||||
id="path67"
|
||||
d="m 105.17203,-43.255454 -8.129199,8.160957 h 23.064239 v -8.160957 z" />
|
||||
</g>
|
||||
</g>
|
||||
</svg>
|
||||
|
After Width: | Height: | Size: 26 KiB |
|
|
@ -13,15 +13,14 @@ singularity {
|
|||
process {
|
||||
beforeScript = 'module load devel/singularity/3.4.2'
|
||||
executor = 'pbs'
|
||||
queue = 'short'
|
||||
process.queue = { task.memory > 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'short' : 'long'}
|
||||
queue = { task.memory >= 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time > 48.h ? 'long' : 'short'}
|
||||
}
|
||||
|
||||
params {
|
||||
igenomes_base = '/nfsmounts/igenomes'
|
||||
max_memory = 1000.GB
|
||||
max_cpus = 28
|
||||
max_time = 48.h
|
||||
max_time = 168.h
|
||||
}
|
||||
|
||||
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.
|
||||
*/
|
||||
|
||||
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.
|
||||
profiles {
|
||||
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
|
||||
|
|
@ -19,11 +16,12 @@ profiles {
|
|||
cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
|
||||
ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
|
||||
ccga_dx { includeConfig "${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" }
|
||||
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
|
||||
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
|
||||
czbiohub_aws_highpriority {
|
||||
includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
|
||||
czbiohub_aws_highpriority {
|
||||
includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
|
||||
includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
|
||||
genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
|
||||
denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
|
||||
|
|
|
|||
|
|
@ -10,4 +10,5 @@
|
|||
|
||||
profiles {
|
||||
munin { includeConfig "${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