From 1eb5757e6ac83367b0043f45921dc24ba2bcceff Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 1 Oct 2019 20:51:45 -0500
Subject: [PATCH] Add ghenry token for Nextflow Tower to biohpc.config and
update Nextflow version (and include tower) in CI
---
.gitlab-ci.yml | 6 +++---
workflow/conf/biohpc.config | 5 +++++
2 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6f8e6ea..3ab69b7 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,7 +2,7 @@ before_script:
- module load astrocyte
- module load python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- - module load nextflow/0.31.1_Ignite
+ - module load nextflow/19.07.0
- mkdir -p test_data/simple1
- mkdir -p test_data/simple2
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/
@@ -26,7 +26,7 @@ astrocyte_check:
simple_1FC:
stage: simple
script:
- - nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv"
+ - nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" -with-tower
- pytest -m simple1
artifacts:
name: "$CI_JOB_NAME"
@@ -43,7 +43,7 @@ simple_1FC:
simple_2FC:
stage: simple
script:
- - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
+ - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" -with-tower
- pytest -m simple2
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 09387c6..fa20501 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -45,3 +45,8 @@ report {
enabled = true
file = 'report.html'
}
+
+tower {
+ accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
+ enabled = true
+}
--
GitLab