From e38e9327f4debee34ac9391d0148dbe80bcf641f Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 26 Nov 2018 17:32:06 +0100 Subject: [PATCH 1/3] Some tidying --- .gitattributes | 1 + .gitignore | 109 ++------------------------------------- conf/binac.config | 1 + conf/cfc.config | 7 +-- conf/hebbe.config | 1 + conf/uppmax-devel.config | 2 +- conf/uppmax.config | 2 +- nfcore_custom.config | 31 +++++------ 8 files changed, 26 insertions(+), 128 deletions(-) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..7fe5500 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +*.config linguist-language=nextflow diff --git a/.gitignore b/.gitignore index 894a44c..07c0144 100644 --- a/.gitignore +++ b/.gitignore @@ -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 diff --git a/conf/binac.config b/conf/binac.config index be69d9e..61450db 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -16,6 +16,7 @@ process { } params { + igenomesIgnore = true max_memory = 128.GB max_cpus = 28 max_time = 48.h diff --git a/conf/cfc.config b/conf/cfc.config index 6285925..40d0049 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -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 diff --git a/conf/hebbe.config b/conf/hebbe.config index 86f8468..e9dcb06 100644 --- a/conf/hebbe.config +++ b/conf/hebbe.config @@ -19,6 +19,7 @@ process { } params { + igenomesIgnore = true saveReference = true max_memory = 64.GB max_cpus = 20 diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config index c77db4a..ef4bb0a 100644 --- a/conf/uppmax-devel.config +++ b/conf/uppmax-devel.config @@ -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 diff --git a/conf/uppmax.config b/conf/uppmax.config index 89fbce1..f19829f 100644 --- a/conf/uppmax.config +++ b/conf/uppmax.config @@ -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 diff --git a/nfcore_custom.config b/nfcore_custom.config index c8b7e6e..a1b324b 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -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" } } From 2c513e52669df1cec7daf7b85ed79abde9716112 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 26 Nov 2018 22:47:36 +0000 Subject: [PATCH 2/3] Update binac.config --- conf/binac.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index 61450db..5d13119 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -6,13 +6,13 @@ */ singularity { - enabled = true + enabled = true } process { - beforeScript = 'module load devel/singularity/3.0.1' - executor = 'pbs' - queue = 'short' + beforeScript = 'module load devel/singularity/3.0.1' + executor = 'pbs' + queue = 'short' } params { From d1f10bba3e8f3b5e0df5bea78ac5f35a31026ad8 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 26 Nov 2018 22:49:03 +0000 Subject: [PATCH 3/3] Update nfcore_custom.config --- nfcore_custom.config | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index a1b324b..7635a9a 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -11,17 +11,16 @@ config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/conf" profiles { - binac { includeConfig "${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" + 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 "${config_base}/uppmax-devel.config" } - uppmax { includeConfig "${config_base}/uppmax.config" } - uzh { includeConfig "${config_base}/uzh.config" } + uppmax { includeConfig "${config_base}/uppmax.config" } + uzh { includeConfig "${config_base}/uzh.config" } }