From 2838803e80b64db4c9e2387e10fa405ac12dc379 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 25 Apr 2020 16:23:50 -0500
Subject: [PATCH] Fix erroneous ci flags
---
.gitlab-ci.yml | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7b2ddfc..19d9073 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -110,7 +110,7 @@ astrocyte_cli:
- master
- tags
script:
- - singularity run 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2 --ci true
+ - singularity run 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -133,8 +133,8 @@ GRCh38-3.0.0:
except:
- tags
script:
- - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
- - pytest -m count310 --ci true
+ - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --ci true
+ - pytest -m count310
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -157,8 +157,8 @@ mm10-3.0.0:
except:
- tags
script:
- - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
- - pytest -m count310 --ci true
+ - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --ci true
+ - pytest -m count310
artifacts:
name: "$CI_JOB_NAME"
when: always
--
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