From 6e617062eb008255a1504dd534caece1bfa227d0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 27 Jan 2021 19:54:29 -0600
Subject: [PATCH] Update reps used for override metadata
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 96a821b..aefc5d1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,6 @@
before_script:
- module load python/3.6.4-anaconda
- - pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1
+ - pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1
- module load singularity/3.5.3
- module load nextflow/20.01.0
- ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
@@ -837,7 +837,7 @@ 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-Y5EP --source staging --speciesForce 'Homo sapiens' --upload false --dev false --ci true --track false -with-report ./speciesOverride_report.html
+ - 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 true --dev false --ci true --track false -with-report ./speciesOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
- pytest -m completionMultiqc --filename speciesOverride_PE_multiqc_data.json
artifacts:
@@ -860,7 +860,7 @@ override_stranded:
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-Y5EP --source staging --strandedForce unstranded --upload false --dev false --ci true --track false -with-report ./strandedOverride_report.html
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EP --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_PE_multiqc_data.json \;
- pytest -m completionMultiqc --filename strandedOverride_PE_multiqc_data.json
artifacts:
@@ -883,7 +883,7 @@ override_spike:
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 --source staging --spikeForce t --upload false --dev false --ci true --track false -with-report ./spikeOverride_report.html
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --spikeForce t --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_PE_multiqc_data.json \;
- pytest -m completionMultiqc --filename spikedOverride_PE_multiqc_data.json
artifacts:
--
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