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Astrocyte
Workflows
Strand Lab
cellranger-count
Commits
d958eade
Commit
d958eade
authored
3 years ago
by
Peng Lian
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Fix blank output file issue
parent
c3042afd
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3 changed files
astrocyte_pkg.yml
+3
-1
3 additions, 1 deletion
astrocyte_pkg.yml
workflow/configs/biohpc.config
+3
-3
3 additions, 3 deletions
workflow/configs/biohpc.config
workflow/main.nf
+11
-6
11 additions, 6 deletions
workflow/main.nf
with
17 additions
and
10 deletions
astrocyte_pkg.yml
+
3
−
1
View file @
d958eade
...
...
@@ -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
:
'
2
0.0
1.0'
nextflow_version
:
'
21.0
4.1
'
# (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
...
...
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workflow/configs/biohpc.config
+
3
−
3
View file @
d958eade
...
...
@@ -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'
}
}
This diff is collapsed.
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workflow/main.nf
+
11
−
6
View file @
d958eade
...
...
@@ -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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