From a50b56877fd4fa4cba516d80b44d6c7e23cc81bc Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 30 Dec 2020 16:03:50 -0600
Subject: [PATCH] Change all integration tests to use staging
---
.gitlab-ci.yml | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f1e4239..572149c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -663,7 +663,7 @@ integration_se:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 -with-dag dag.png --ci true --email 'venkat.malladi@utsouthwestern.edu,Gervaise.Henry@UTSouthwestern.edu'
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging -with-dag dag.png --ci true --email 'venkat.malladi@utsouthwestern.edu,Gervaise.Henry@UTSouthwestern.edu'
- find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
@@ -687,7 +687,7 @@ integration_pe:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA -with-dag dag.png --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging -with-dag dag.png --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
@@ -713,7 +713,7 @@ override_inputBag:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
@@ -735,7 +735,7 @@ override_fastq:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
@@ -757,7 +757,7 @@ override_species:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --speciesForce 'Homo sapiens' --upload false --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --speciesForce 'Homo sapiens' --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
--
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