Merge pull request #711 from MaxUlysse/Munin

Improve configuration file priorities

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Changed`
 
 -   [#710](https://github.com/SciLifeLab/Sarek/pull/710) - Improve release checklist and script
+-   [#711](https://github.com/SciLifeLab/Sarek/pull/711) - Improve configuration priorities
 
 ## [2.2.2] - 2018-12-19
 

conf/base.config

@@ -10,7 +10,6 @@ wf_repository = 'maxulysse'
 
 params {
   // set up default params
-  containerPath = '' // Path to Singularity images
   docker = false // Don't use Docker to build buildContainers.nf
   download = false // Don't download reference files in buildReferences.nf
   explicitBqsrNeeded = true // Enable recalibration in main.nf

conf/munin.config

@@ -11,6 +11,7 @@ env {
 }
 
 params {
+  containerPath = '/btb/containers/'
   genome_base = params.genome == 'GRCh37' ? '/btb/references/Homo_sapiens/GATK/GRCh37/' : params.genome == 'GRCh38' ? '/btb/references/Homo_sapiens/GATK/GRCh38/' : 'References/smallGRCh37'
   singleCPUMem  = 15.GB
   totalMemory = 754.GB

docs/CONFIG.md

@@ -90,16 +90,6 @@ The default profile is `standard`, but Sarek has multiple predefined profiles wh
 ```bash
 nextflow run SciLifeLab/Sarek --sample mysample.tsv -profile myprofile
 ```
-awsbatch {
-binac {
-btb {
-cfc {
-docker {
-singularity {
-singularityPath {
-slurm {
-slurmDownload {
-standard {
 
 ### `awsbatch`
 
@@ -136,18 +126,12 @@ Singularity images needs to be set up.
 
 This is another profile for use on a UPPMAX cluster using the job scheduler slurm with Singularity.
 Will run the workflow on `/scratch`.
-Singularity images need to be set up.
-
-### `slurmDownload`
-
-This is another profile for use on a UPPMAX cluster using the job scheduler slurm with Singularity.
-Will run the workflow on `/scratch`.
-Singularity images will be pulled automatically.
+Singularity images are already set up.
 
 ### `standard`
 
 This is the default profile for use on a localhost on a UPPMAX cluster with Singularity.
-Singularity images need to be set up.
+Singularity images are already set up.
 
 ## Customisation
 The recommended way to use custom settings is to supply Sarek with an additional configuration file. You can use the files in the [`conf/`](https://github.com/SciLifeLab/Sarek/tree/master/conf) directory as an inspiration to make this new `.config` file and specify it using the `-c` flag:

docs/INSTALL_BIANCA.md

@@ -58,14 +58,12 @@ For more information about using Singularity with UPPMAX, follow the [Singularit
 ## Install Sarek
 
 Sarek use Singularity containers to package all the different tools.
-All containers are already stored on UPPMAX.
+All containers, and all Reference files are already stored on UPPMAX.
 
 As `bianca` is secure, no direct download is available, so Sarek will have to be installed and updated manually.
 
 You can either download Sarek on your computer or on `rackham`, make an archive, and send it to `bianca` using `FileZilla` or `sftp` given your preferences.
 
-All Reference files are already stored in `bianca`.
-
 ```bash
 # Connect to rackham
 > ssh -AX [USER]@rackham.uppmax.uu.se

docs/INSTALL_RACKHAM.md

@@ -8,16 +8,17 @@ This workflow itself needs little installation.
 
 You need to install [Nextflow][nextflow-link] and put it somewhere in your `$PATH`
 
-The Reference files are already stored in `rackham`.
+Sarek use Singularity containers to package all the different tools.
+
+All containers, and all Reference files are already stored on UPPMAX.
 
 Nextflow will automatically fetch Sarek from GitHub when launched if `SciLifeLab/Sarek` is specified as the workflow name.
 
-Sarek use Singularity containers to package all the different tools.
-All containers are already stored on UPPMAX.
 
 ## Test Sarek with small dataset and small reference
 
-For more information, follow the [reference files documentation](REFERENCES.md). The following tutorial explain how to run Sarek on a small dataset using a small reference.
+For more information, follow the [reference files documentation](REFERENCES.md).
+The following tutorial explain how to run Sarek on a small dataset using a small reference.
 
 ```bash
 # Connect to rackham
@@ -45,10 +46,10 @@ For more information, follow the [reference files documentation](REFERENCES.md).
 > cd test_Sarek
 
 # Build the smallGRCh37 reference
-> nextflow run SciLifeLab/Sarek/buildReferences.nf --download --genome smallGRCh37 --project [PROJECT] -profile download
+> nextflow run SciLifeLab/Sarek/buildReferences.nf --download --genome smallGRCh37 --project [PROJECT]
 
 # Test the workflow on a test tiny set
-> nextflow run SciLifeLab/Sarek --test --genome smallGRCh37 --noReports --project [PROJECT] -profile download
+> nextflow run SciLifeLab/Sarek --test --genome smallGRCh37 --noReports --project [PROJECT]
 ```
 
 ## Update Sarek
@@ -63,12 +64,12 @@ For more information, follow the [reference files documentation](REFERENCES.md).
 
 ## Use Sarek with slurm
 
-To use Sarek on rackham you will need to use the `slurmDownload` profile.
+To use Sarek on rackham you will need to use the `slurm` profile.
 
 ```bash
 # Connect to rackham
 > ssh -AX [USER]@rackham.uppmax.uu.se
 
 # Run the workflow directly on the login node
-> nextflow run SciLifeLab/Sarek/main.nf --project [PROJECT] -profile slurmDownload
+> nextflow run SciLifeLab/Sarek/main.nf --project [PROJECT] -profile slurm
 ```

nextflow.config

@@ -27,9 +27,9 @@ profiles {
   // Docker images will be pulled automatically
   awsbatch {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/igenomes.config'
     includeConfig 'conf/aws-batch.config'
     includeConfig 'conf/docker.config'
+    includeConfig 'conf/igenomes.config'
     includeConfig 'conf/resources.config'
     includeConfig 'conf/containers.config'
   }
@@ -49,8 +49,8 @@ profiles {
   // Singularity images need to be set up
   btb {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/igenomes.config'
     includeConfig 'conf/munin.config'
+    includeConfig 'conf/igenomes.config'
     includeConfig 'conf/singularity-path.config'
   }
   // Default config for CFC cluster in Tuebingen/Germany
@@ -66,59 +66,48 @@ profiles {
   // Docker images will be pulled automatically
   docker {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/genomes.config'
     includeConfig 'conf/travis.config'
+    includeConfig 'conf/genomes.config'
     includeConfig 'conf/docker.config'
     includeConfig 'conf/containers.config'
   }
   // Small testing with Singularity profile
   // Singularity images will be pulled automatically
   singularity {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/genomes.config'
     includeConfig 'conf/travis.config'
+    includeConfig 'conf/genomes.config'
     includeConfig 'conf/singularity.config'
     includeConfig 'conf/containers.config'
   }
   // Small testing with Singularity profile
   // Singularity images need to be set up
   singularityPath {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/genomes.config'
     includeConfig 'conf/travis.config'
+    includeConfig 'conf/genomes.config'
     includeConfig 'conf/singularity-path.config'
   }
   // slurm profile for UPPMAX secure clusters
   // Runs the pipeline using the job scheduler
-  // Singularity images need to be set up
+  // Singularity images are already set up
   slurm {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/genomes.config'
     includeConfig 'conf/uppmax-slurm.config'
-    includeConfig 'conf/singularity-path.config'
-  }
-  // slurm profile for UPPMAX clusters
-  // Runs the pipeline using the job scheduler
-  // Singularity images will be pulled automatically
-  slurmDownload {
-    includeConfig 'conf/base.config'
     includeConfig 'conf/genomes.config'
-    includeConfig 'conf/uppmax-slurm.config'
-    includeConfig 'conf/singularity.config'
-    includeConfig 'conf/containers.config'
+    includeConfig 'conf/singularity-path.config'
   }
   // Default profile for UPPMAX secure clusters
   // Runs the pipeline locally on a single 16-core node
-  // Singularity images need to be set up
+  // Singularity images are already set up
   standard {
     includeConfig 'conf/base.config'
-    includeConfig 'conf/genomes.config'
     includeConfig 'conf/uppmax-localhost.config'
+    includeConfig 'conf/genomes.config'
     includeConfig 'conf/singularity-path.config'
   }
 }
 
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {