Commit bf87d199 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

Merge branch 'singularity' of git.biohpc.swmed.edu:BICF/Astrocyte/rnaseq into singularity

parents b5e2828c 2a49ed98
Pipeline #10009 canceled with stage
in 69 minutes and 42 seconds
# Gitlab CI Script for astrocyte/rnaseq # Gitlab CI Script for astrocyte/rnaseq
# Brandi L. Cantarel - 2017 # Brandi L. Cantarel - 2017
variables:
GIT_SUBMODULE_STRATEGY: recursive
before_script: before_script:
- module load nextflow/0.31.0 - module load nextflow/20.01.0
- git submodule sync --recursive - module load singularity/3.0.2
- git submodule update --init --recursive
stages: stages:
- integration - integration
...@@ -12,13 +14,13 @@ stages: ...@@ -12,13 +14,13 @@ stages:
test_human: test_human:
stage: integration stage: integration
script: script:
- nextflow run -with-dag flowchart.png -with-timeline human_timeline.html -with-report human_report.html workflow/main.nf --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output - nextflow run -c nextflow.config -with-dag flowchart.png -with-timeline human_timeline.html -with-report human_report.html workflow/main.nf --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
test_mouse: test_mouse:
stage: integration stage: integration
script: script:
- nextflow run -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html workflow/main.nf --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/mouse/GRCm38 --markdups null --output mouse_output - nextflow run -c nextflow.config -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html workflow/main.nf --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/mouse/GRCm38 --markdups null --output mouse_output
artifacts: artifacts:
expire_in: 2 days expire_in: 2 days
[submodule "workflow/process_scripts"] [submodule "workflow/process_scripts"]
path = workflow/process_scripts path = workflow/process_scripts
url = git@git.biohpc.swmed.edu:ngsclialab/process_scripts.git url = ../../../ngsclialab/process_scripts.git
...@@ -40,7 +40,7 @@ process { ...@@ -40,7 +40,7 @@ process {
singularity { singularity {
enabled = true enabled = true
runOptions='--no-home --cleanenv' runOptions='--no-home --cleanenv'
cacheDir="$PWD" singularity.cacheDir="$PWD"
} }
trace { trace {
......
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