Commit d958eade authored by Peng Lian's avatar Peng Lian
Browse files

Fix blank output file issue

parent c3042afd
Pipeline #10602 failed with stages
......@@ -35,7 +35,7 @@ minimum_astrocyte_version: '0.4.1'
# The Nextflow version that requires to run this workflow. For old pipelines, which do not have this label
# a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
# in the module list.
nextflow_version: '20.01.0'
nextflow_version: '21.04.1'
# (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
nextflow_config: 'biohpc.config'
# The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
......@@ -176,6 +176,8 @@ vizapp_r_module: 'R/3.6.1-gccmkl'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_cran_packages:
- shiny
- shinyFiles
- plotly
# # List of any Bioconductor packages, not provided by the modules, that must be made
......
......@@ -8,12 +8,12 @@ singularity {
process {
executor = 'local'
withName:uppercase {
container = 'ubuntu:latest'
container = 'docker://ubuntu:latest'
}
withName:tolines {
container = 'ubuntu:latest'
container = 'docker://ubuntu:latest'
}
withName:wordcounts {
container = 'centos:centos8'
container = 'docker://centos:centos8'
}
}
......@@ -6,7 +6,7 @@
* This is a minimal test workflow package that astrocyte tests can run against.
*
* @authors
* David Trudgian <David.Trudgian@UTSouthwestern.edu>
* David Trudgian, Peng Lian, Devin OKelly
*
*/
......@@ -27,9 +27,13 @@ stories = Channel.fromPath( params.story )
process parameters {
cpus 1
//container 'ubuntu:latest'
"""
echo ""
echo "This script is running on:"
cat /etc/os-release
echo ""
echo "Test Parameters Provided..."
echo "story: ${params.story}"
echo "test_int: ${params.test_int}"
......@@ -37,9 +41,6 @@ process parameters {
echo "test_string: ${params.test_string}"
echo "test_select: ${params.test_select}"
echo "test_multiselect: ${params.test_multiselect}"
pwd
whoami
env
"""
}
......@@ -77,7 +78,6 @@ process tolines {
process wordcounts {
// Publish the outputs we create here into the workflow output directory
publishDir "$baseDir/output", mode: 'copy'
......@@ -88,6 +88,11 @@ process wordcounts {
file "${wordlines.name}.wordcount"
"""
echo ""
echo "This script is running on:"
cat /etc/os-release
echo ""
cat "$wordlines" | sort | uniq -c | sort -n -r > "${wordlines.name}.wordcount"
"""
}
......
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