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Commit 4c1b2f4e authored by Peng Lian's avatar Peng Lian
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Run with Singularity container

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workflow/configs/biohpc.config
+ 6
− 5
View file @ 4c1b2f4e
process { singularity {
executor = 'local' enabled = true
runOptions = '--bind /vagrant:/vagrant'
cacheDir = "$baseDir/images/singularity"
} }
executor { process {
name = 'local' executor = 'local'
cpus = 1
} }
workflow/main.nf
+ 5
− 0
View file @ 4c1b2f4e
...@@ -27,6 +27,7 @@ stories = Channel.fromPath( params.story ) ...@@ -27,6 +27,7 @@ stories = Channel.fromPath( params.story )
process parameters { process parameters {
cpus 1 cpus 1
container 'ubuntu:latest'
""" """
echo "Test Parameters Provided..." echo "Test Parameters Provided..."
...@@ -43,6 +44,7 @@ process parameters { ...@@ -43,6 +44,7 @@ process parameters {
process uppercase { process uppercase {
cpus 1 cpus 1
container 'ubuntu:latest'
input: input:
file story from stories file story from stories
...@@ -59,6 +61,7 @@ process uppercase { ...@@ -59,6 +61,7 @@ process uppercase {
process tolines { process tolines {
cpus 1 cpus 1
container 'ubuntu:latest'
input: input:
file uppercase from uppercased file uppercase from uppercased
...@@ -74,6 +77,8 @@ process tolines { ...@@ -74,6 +77,8 @@ process tolines {
process wordcounts { process wordcounts {
container 'ubuntu:latest'
// Publish the outputs we create here into the workflow output directory // Publish the outputs we create here into the workflow output directory
publishDir "$baseDir/output", mode: 'copy' publishDir "$baseDir/output", mode: 'copy'
......
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