From 82dafd86359332668f396bfb99f40ff30d1368c7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 22 Mar 2019 11:37:55 -0500
Subject: [PATCH] Create simple CI
---
.gitlab-ci.yml | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1e33971..9340788 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,29 +2,37 @@ before_script:
- module load astrocyte
- module load python/3.6.1-2-anaconda
- module load nextflow/0.31.1_Ignite
+ - mkdir test_data/hu.v2s1r1k
- mkdir test_data/mu.v2s2r10k
- mkdir test_data/hu.v3s2r10k
+ - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v2s1r1k/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
stages:
- astrocyte
- - run
+ - simple
+ - detailed
astrocyte_check:
stage: astrocyte
script:
- astrocyte_cli check ../cellranger_count
+run_hu.cr3v2ref3.0.0:
+ stage: simple
+ script:
+ - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+
run_mu.cr2v2ref1.2.0:
- stage: run
+ stage: detailed
except:
- tags
script:
- nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'two' --version '2.1.1'
run_hu.cr3v3ref3.0.0:
- stage: run
+ stage: detailed
except:
- tags
script:
--
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