Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
C
cellranger-count
Manage
Activity
Members
Labels
Plan
Issues
3
Issue boards
Milestones
Iterations
Wiki
Requirements
Code
Merge requests
0
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Locked files
Build
Pipelines
Jobs
Pipeline schedules
Test cases
Artifacts
Deploy
Releases
Package Registry
Container Registry
Operate
Environments
Terraform modules
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Code review analytics
Issue analytics
Insights
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Astrocyte
Workflows
Strand Lab
cellranger-count
Commits
0bbe0bf3
Commit
0bbe0bf3
authored
4 years ago
by
PLian
Browse files
Options
Downloads
Patches
Plain Diff
Update yaml file
parent
416472ba
Branches
Branches containing commit
Tags
Tags containing commit
No related merge requests found
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
.gitignore
+1
-0
1 addition, 0 deletions
.gitignore
.gitlab-ci.yml
+1
-1
1 addition, 1 deletion
.gitlab-ci.yml
astrocyte_pkg.yml
+6
-3
6 additions, 3 deletions
astrocyte_pkg.yml
workflow/configs/biohpc.config
+4
-0
4 additions, 0 deletions
workflow/configs/biohpc.config
with
12 additions
and
4 deletions
.gitignore
+
1
−
0
View file @
0bbe0bf3
...
...
@@ -2,3 +2,4 @@ workflow/work
workflow/*.html
workflow/*.csv
.history
This diff is collapsed.
Click to expand it.
.gitlab-ci.yml
+
1
−
1
View file @
0bbe0bf3
# Run our tests against a specific version of astrocyte
before_script
:
-
module load astrocyte/0.
1
.0
-
module load astrocyte/0.
4
.0
stages
:
...
...
This diff is collapsed.
Click to expand it.
astrocyte_pkg.yml
+
6
−
3
View file @
0bbe0bf3
...
...
@@ -9,7 +9,7 @@
# A unique identifier for the workflow package, text/underscores only
name
:
'
example_wordcount'
# Who wrote this?
author
:
'
David
Trudgian'
author
:
'
David
Trudgian
,
Peng
Lian
'
# A contact email address for questions
email
:
'
biohpc-help@utsouthwestern.edu'
# A more informative title for the workflow package
...
...
@@ -18,15 +18,18 @@ title: 'Example Wordcount Workflow'
description
:
|
This is a minimal test workflow package that counts the occurences of words
in a test file. It can be used as a template to develop workflows, and as to
test the astrocyte platform.
test the astrocyte platform. Please note that start from publish version
0.0.8 and test version 0.0.2, this workflow will only support Astrocyte 0.4.0
and above.
#### New Features in Astrocyte 0.4.0 and above ####
# The Astrocyte version it requires to run this workflow
astrocyte_version
:
'
0.4.0'
# The Nextflow version it requires to run this workflow
nextflow_version
:
'
20.01.0'
# (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 mi
ssing
the default value 'none' will be used.
# The container to use for this workflow, none/singularity. If
o
mi
tted,
the default value 'none' will be used.
container
:
'
singularity'
# The version of singularity to use. This is required if container == 'singularity'
singularity_version
:
'
3.5.3'
...
...
This diff is collapsed.
Click to expand it.
workflow/configs/biohpc.config
+
4
−
0
View file @
0bbe0bf3
process
{
executor
=
'local'
}
executor
{
name
=
'local'
cpus
=
1
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment