From d72024dcce53e5e1bdd2ea0e445698509bd0073c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 23 Jul 2019 10:40:03 -0500
Subject: [PATCH] Run simple3 test (hv2s1) with 1k reads, and set simple1 test
(h3s1) to auto chemistry
---
.gitlab-ci.yml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e252f7a..e8a6df1 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -10,7 +10,7 @@ before_script:
- mkdir test_data/mu.v3s2r10k
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s1r500/* test_data/hu.v3s1r500/
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s1r500/* test_data/mu.v3s1r500/
- - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
+ - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r1k/* test_data/hu.v2s1r1k/
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s2r10k/* test_data/mu.v3s2r10k/
@@ -37,7 +37,7 @@ simple_1:
except:
- master
script:
- - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
+ - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
- pytest -m count302
artifacts:
name: "$CI_JOB_NAME"
@@ -77,7 +77,7 @@ simple_3:
except:
- master
script:
- - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r500/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+ - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r1k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
- pytest -m count211
artifacts:
name: "$CI_JOB_NAME"
--
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