diff --git a/README.md b/README.md index 3a921372bf..4676fc6a12 100644 --- a/README.md +++ b/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) -------------------------------------------------------------------------------- diff --git a/configuration/base.config b/configuration/base.config index 695f3c91da..11899166c9 100644 --- a/configuration/base.config +++ b/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 diff --git a/doc/INSTALL.md b/doc/INSTALL.md index f5f87012fa..4dccd9a327 100644 --- a/doc/INSTALL.md +++ b/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.