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