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
8619ed5e
Commit
8619ed5e
authored
1 year ago
by
John Lafin
Browse files
Options
Downloads
Patches
Plain Diff
fix sample and id for barnyard
parent
aed9ea90
Branches
Branches containing commit
Tags
Tags containing commit
1 merge request
!2
Ci
Pipeline
#13579
passed with stages
in 27 minutes and 37 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
.gitlab-ci.yml
+12
-2
12 additions, 2 deletions
.gitlab-ci.yml
with
12 additions
and
2 deletions
.gitlab-ci.yml
+
12
−
2
View file @
8619ed5e
...
@@ -25,7 +25,11 @@ test-count-human: # Run cellranger count on the human data
...
@@ -25,7 +25,11 @@ test-count-human: # Run cellranger count on the human data
before_script
:
before_script
:
-
export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
-
export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
script
:
script
:
-
nextflow run workflow/main.nf --reference=/data/ref_data/refdata-gex-GRCh38-2020-A --fastq=/data/test_data/Brain_Tumor_3p_LT_fastqs --noBam=true
-
>
nextflow run workflow/main.nf
--reference=/data/ref_data/refdata-gex-GRCh38-2020-A
--fastq=/data/test_data/Brain_Tumor_3p_LT_fastqs
--noBam=true
-
nextflow clean -f -keep-logs
-
nextflow clean -f -keep-logs
test-count-barnyard
:
# Run cellranger count on the barnyard data
test-count-barnyard
:
# Run cellranger count on the barnyard data
...
@@ -36,5 +40,11 @@ test-count-barnyard: # Run cellranger count on the barnyard data
...
@@ -36,5 +40,11 @@ test-count-barnyard: # Run cellranger count on the barnyard data
before_script
:
before_script
:
-
export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
-
export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
script
:
script
:
-
nextflow run workflow/main.nf --fastq=/data/test_data/hgmm_100_fastqs --reference=/data/ref_data/refdata-gex-GRCh38-and-mm10-2020-A --noBam=true
-
>
nextflow run workflow/main.nf
--id=hgmm_100
--sample=hgmm_100
--fastq=/data/test_data/hgmm_100_fastqs
--reference=/data/ref_data/refdata-gex-GRCh38-and-mm10-2020-A
--noBam=true
-
nextflow clean -f -keep-logs
-
nextflow clean -f -keep-logs
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