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