Merge pull request nf-core#585 from szilvajuhos/master

Minor doc changes

Author: Szilveszter Juhos

README.md

@@ -98,7 +98,6 @@ For further information or help, don't hesitate to get in touch on [Gitter][gitt
 * [Marcel Martin](https://github.com/marcelm)
 * [Björn Nystedt](https://github.com/bjornnystedt)
 * [Pall Olason](https://github.com/pallolason)
-* [Pelin Sahlén](https://github.com/pelinakan)
 
 --------------------------------------------------------------------------------
 

configuration/base.config

@@ -71,7 +71,7 @@ timeline { // Turning on timeline tracking by default
 trace { // Turning on trace tracking by default
   enabled = true
   fields = 'process,task_id,hash,name,attempt,status,exit,realtime,%cpu,vmem,rss,submit,start,complete,duration,realtime,rchar,wchar'
-  file = "${params.outDir}/Reports/Sarek_trace.html"
+  file = "${params.outDir}/Reports/Sarek_trace.txt"
 }
 
 // Function to ensure that resource requirements don't go beyond

doc/INSTALL.md

@@ -26,46 +26,13 @@ export NXF_SINGULARITY_CACHEDIR=$HOME/.singularity
 
 Docker can also be used as a container technology.
 
-## Test Sarek with small dataset and small reference
+You can [Test Sarek with small dataset and small reference](https://github.com/SciLifeLab/Sarek/blob/master/doc/TESTS.md)
 
-The following tutorial explain how to run Sarek on a small dataset using a small reference.
-
-```bash
-# Connect to your system
-> ssh -AX [USER]@[system]
-# Or just open a terminal
-
-# Install Nextflow
-> curl -s https://get.nextflow.io | bash
-
-# Move Nextflow into your $PATH
-> mv nextflow $HOME/bin
-
-# Set up the cache directory for Singularity Images if needed
-> export NXF_SINGULARITY_CACHEDIR=$HOME/.singularity
-
-# make a test directory
-> mkdir test_Sarek
-> cd test_Sarek
-
-# Download and build the smallGRCh37 reference using Singularity
-> nextflow run SciLifeLab/Sarek/buildReferences.nf --download --genome smallGRCh37 -profile singularity
-
-# Or download and build the smallGRCh37 reference using Docker
-> nextflow run SciLifeLab/Sarek/buildReferences.nf --download --genome smallGRCh37 -profile docker
-
-# Test Sarek on a test tiny set using Singularity
-> nextflow run SciLifeLab/Sarek/main.nf --test --genome smallGRCh37 --noReports -profile singularity
-
-# Or test Sarek on a test tiny set using Docker
-> nextflow run SciLifeLab/Sarek/main.nf --test --genome smallGRCh37 --noReports -profile docker
-```
-
-## Update
+## Update		
 
 To update Sarek, it's also very simple:
 
-
+ 
 ```bash
 # Connect to your system
 > ssh -AX [USER]@[system]REFERENCES
@@ -75,7 +42,7 @@ To update Sarek, it's also very simple:
 > nextflow pull SciLifeLab/Sarek
 ```
 
-## Run Sarek on real data
+## Running Sarek with real data
 
 Follow the [references documentation](REFERENCES.md) on how to download/build the references files.