Merge pull request #4 from ewels/master

Some tidying

.gitattributes

@@ -0,0 +1 @@
+*.config linguist-language=nextflow

.gitignore

@@ -1,104 +1,5 @@
-# Byte-compiled / optimized / DLL files
+.nextflow*
-__pycache__/
+work/
-*.py[cod]
+data/
-*$py.class
+results/
-
+.DS_Store
-# 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/

conf/binac.config

@@ -6,16 +6,17 @@
  */
 
 singularity {
-    enabled = true
+  enabled = true
 }
 
 process {
-    beforeScript = 'module load devel/singularity/3.0.1'
+  beforeScript = 'module load devel/singularity/3.0.1'
-    executor = 'pbs'
+  executor = 'pbs'
-    queue = 'short'
+  queue = 'short'
 }
 
 params {
+  igenomesIgnore = true
   max_memory = 128.GB
   max_cpus = 28
   max_time = 48.h

conf/cfc.config

@@ -6,15 +6,16 @@
  */
 
 singularity {
-    enabled = true
+  enabled = true
 }
 
 process {
-    beforeScript = 'module load qbic/singularity_slurm/3.0.1'
+  beforeScript = 'module load qbic/singularity_slurm/3.0.1'
-    executor = 'slurm'
+  executor = 'slurm'
 }
 
 params {
+  igenomesIgnore = true
   max_memory = 60.GB
   max_cpus = 24
   max_time = 140.h

conf/hebbe.config

@@ -19,6 +19,7 @@ process {
 }
 
 params {
+  igenomesIgnore = true
   saveReference = true
   max_memory = 64.GB
   max_cpus = 20

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

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

nfcore_custom.config

@@ -11,24 +11,16 @@
 config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/conf"
 
 profiles {
-
+  binac        { includeConfig "${config_base}/binac.config" }
-  binac { includeConfig "${config_base}/binac.config"
+  ccga         { includeConfig "${config_base}/ccga.config" }
-    	  params.igenomesIgnore = true
+  cfc          { includeConfig "${config_base}/cfc.config" }
-  }
+  crick        { includeConfig "${config_base}/crick.config" }
-  ccga { includeConfig "${config_base}/ccga.config" }
+  gis          { includeConfig "${config_base}/gis.config" }
-  cfc { includeConfig "${config_base}/cfc.config"
+  hebbe        { includeConfig "${config_base}/hebbe.config" }
-        params.igenomesIgnore = true
+  uct_hex      { includeConfig "${config_base}/uct_hex.config" }
-  }
-  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"
+                 includeConfig "${config_base}/uppmax-devel.config"
   }
-  uppmax { includeConfig "${config_base}/uppmax.config" }
+  uppmax       { includeConfig "${config_base}/uppmax.config" }
-  uzh { includeConfig "${config_base}/uzh.config" }
+  uzh          { includeConfig "${config_base}/uzh.config" }
-    
 }