mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-30 11:12:10 -05:00
Some tidying
This commit is contained in:
Phil Ewels
parent
1bf45362e5
commit
e38e9327f4
8 changed files with 26 additions and 128 deletions
1
.gitattributes
vendored
Normal file
1
.gitattributes
vendored
Normal file
|
|
@ -0,0 +1 @@
|
|||
*.config linguist-language=nextflow
|
||||
109
.gitignore
vendored
109
.gitignore
vendored
|
|
@ -1,104 +1,5 @@
|
|||
# Byte-compiled / optimized / DLL files
|
||||
__pycache__/
|
||||
*.py[cod]
|
||||
*$py.class
|
||||
|
||||
# C extensions
|
||||
*.so
|
||||
|
||||
# Distribution / packaging
|
||||
.Python
|
||||
build/
|
||||
develop-eggs/
|
||||
dist/
|
||||
downloads/
|
||||
eggs/
|
||||
.eggs/
|
||||
lib/
|
||||
lib64/
|
||||
parts/
|
||||
sdist/
|
||||
var/
|
||||
wheels/
|
||||
*.egg-info/
|
||||
.installed.cfg
|
||||
*.egg
|
||||
MANIFEST
|
||||
|
||||
# PyInstaller
|
||||
# Usually these files are written by a python script from a template
|
||||
# before PyInstaller builds the exe, so as to inject date/other infos into it.
|
||||
*.manifest
|
||||
*.spec
|
||||
|
||||
# Installer logs
|
||||
pip-log.txt
|
||||
pip-delete-this-directory.txt
|
||||
|
||||
# Unit test / coverage reports
|
||||
htmlcov/
|
||||
.tox/
|
||||
.coverage
|
||||
.coverage.*
|
||||
.cache
|
||||
nosetests.xml
|
||||
coverage.xml
|
||||
*.cover
|
||||
.hypothesis/
|
||||
.pytest_cache/
|
||||
|
||||
# Translations
|
||||
*.mo
|
||||
*.pot
|
||||
|
||||
# Django stuff:
|
||||
*.log
|
||||
local_settings.py
|
||||
db.sqlite3
|
||||
|
||||
# Flask stuff:
|
||||
instance/
|
||||
.webassets-cache
|
||||
|
||||
# Scrapy stuff:
|
||||
.scrapy
|
||||
|
||||
# Sphinx documentation
|
||||
docs/_build/
|
||||
|
||||
# PyBuilder
|
||||
target/
|
||||
|
||||
# Jupyter Notebook
|
||||
.ipynb_checkpoints
|
||||
|
||||
# pyenv
|
||||
.python-version
|
||||
|
||||
# celery beat schedule file
|
||||
celerybeat-schedule
|
||||
|
||||
# SageMath parsed files
|
||||
*.sage.py
|
||||
|
||||
# Environments
|
||||
.env
|
||||
.venv
|
||||
env/
|
||||
venv/
|
||||
ENV/
|
||||
env.bak/
|
||||
venv.bak/
|
||||
|
||||
# Spyder project settings
|
||||
.spyderproject
|
||||
.spyproject
|
||||
|
||||
# Rope project settings
|
||||
.ropeproject
|
||||
|
||||
# mkdocs documentation
|
||||
/site
|
||||
|
||||
# mypy
|
||||
.mypy_cache/
|
||||
.nextflow*
|
||||
work/
|
||||
data/
|
||||
results/
|
||||
.DS_Store
|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ process {
|
|||
}
|
||||
|
||||
params {
|
||||
igenomesIgnore = true
|
||||
max_memory = 128.GB
|
||||
max_cpus = 28
|
||||
max_time = 48.h
|
||||
|
|
|
|||
|
|
@ -6,15 +6,16 @@
|
|||
*/
|
||||
|
||||
singularity {
|
||||
enabled = true
|
||||
enabled = true
|
||||
}
|
||||
|
||||
process {
|
||||
beforeScript = 'module load qbic/singularity_slurm/3.0.1'
|
||||
executor = 'slurm'
|
||||
beforeScript = 'module load qbic/singularity_slurm/3.0.1'
|
||||
executor = 'slurm'
|
||||
}
|
||||
|
||||
params {
|
||||
igenomesIgnore = true
|
||||
max_memory = 60.GB
|
||||
max_cpus = 24
|
||||
max_time = 140.h
|
||||
|
|
|
|||
|
|
@ -19,6 +19,7 @@ process {
|
|||
}
|
||||
|
||||
params {
|
||||
igenomesIgnore = true
|
||||
saveReference = true
|
||||
max_memory = 64.GB
|
||||
max_cpus = 20
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
/*
|
||||
* -------------------------------------------------
|
||||
* Nextflow config file for UPPMAX (milou / irma)
|
||||
* Nextflow config file for UPPMAX (rackham / irma)
|
||||
* -------------------------------------------------
|
||||
* To be applied after main UPPMAX config, overwrites config and
|
||||
* submits jobs to the `devcore` queue, which has much faster
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
/*
|
||||
* -------------------------------------------------
|
||||
* Nextflow config file for UPPMAX (milou / irma)
|
||||
* Nextflow config file for UPPMAX (rackham / irma)
|
||||
* -------------------------------------------------
|
||||
* Defines reference genomes, using iGenome paths
|
||||
* Imported under the default 'standard' Nextflow
|
||||
|
|
|
|||
|
|
@ -11,24 +11,17 @@
|
|||
config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/conf"
|
||||
|
||||
profiles {
|
||||
|
||||
binac { includeConfig "${config_base}/binac.config"
|
||||
params.igenomesIgnore = true
|
||||
binac { includeConfig "${config_base}/binac.config" }
|
||||
ccga { includeConfig "${config_base}/ccga.config" }
|
||||
cfc { includeConfig "${config_base}/cfc.config" }
|
||||
crick { includeConfig "${config_base}/crick.config" }
|
||||
gis { includeConfig "${config_base}/gis.config" }
|
||||
hebbe { includeConfig "${config_base}/hebbe.config" }
|
||||
uct_hex { includeConfig "${config_base}/uct_hex.config" }
|
||||
uppmax_devel {
|
||||
includeConfig "${config_base}/uppmax.config"
|
||||
includeConfig "${config_base}/uppmax-devel.config"
|
||||
}
|
||||
ccga { includeConfig "${config_base}/ccga.config" }
|
||||
cfc { includeConfig "${config_base}/cfc.config"
|
||||
params.igenomesIgnore = true
|
||||
}
|
||||
crick { includeConfig "${config_base}/crick.config" }
|
||||
gis { includeConfig "${config_base}/gis.config" }
|
||||
hebbe { includeConfig "${config_base}/hebbe.config"
|
||||
params.igenomesIgnore = true
|
||||
}
|
||||
uct_hex { includeConfig "${config_base}/uct_hex.config" }
|
||||
uppmax_devel { includeConfig "${config_base}/uppmax.config"
|
||||
includeConfig "${config_base}/uppmax-devel.config"
|
||||
}
|
||||
uppmax { includeConfig "${config_base}/uppmax.config" }
|
||||
uzh { includeConfig "${config_base}/uzh.config" }
|
||||
|
||||
uppmax { includeConfig "${config_base}/uppmax.config" }
|
||||
uzh { includeConfig "${config_base}/uzh.config" }
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue