Merge pull request #6 from UMCUGenetics/release/v1.1.1

Release/v1.1.1
UMCUGenetics · Aug 19, 2021 · 2b00df5 · 2b00df5
2 parents cdff64b + 0b03b1a
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diff --git a/README.md b/README.md
@@ -1,6 +1,22 @@
 # DxNextflowWGS
 Genome Diagnostics Nextflow WGS workflow
 
+## Get Nextflow Modules
+```bash
+git submodule update --init --recursive
+```
+
+## Install Nextflow
+```bash
+mkdir tools && cd tools
+curl -s https://get.nextflow.io | bash
+```
+
+## Running WGS workflow
+```bash
+nextflow run WGS.nf -c WGS.config --fastq_path <fastq_dir_path> --outdir <output_dir_path> --email <email> [-profile slurm|mac]
+```
+
 ## QDNAseq GUIX container
 ```bash
 guixr pack -f squashfs -RR -S /bin=bin r r-qdnaseq-hmf r-getoptlong perl bash glibc-utf8-locales tzdata coreutils procps grep sed bootstrap-binaries

diff --git a/WGS.config b/WGS.config
@@ -285,6 +285,9 @@ profiles {
 
         executor {
             queueSize = 1000
+            pollInterval = '1min'
+            queueStatInterval = '5min'
+            submitRatelimit = '10sec'
         }
     }