From 63fbe5e4ae0d2747b8220ab4933067c71cb0d14f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 28 Jan 2021 09:34:32 -0600
Subject: [PATCH] Fix spike override test
---
.gitlab-ci.yml | 30 +++++++++++++++---------------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4fe24a0..f794c79 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -792,13 +792,13 @@ override_inputBag:
- 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 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
- - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
- - pytest -m completionMultiqc --filename inputBagOverride_PE_multiqc_data.json
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_multiqc_data.json \;
+ - pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- - inputBagOverride_PE_multiqc_data.json
+ - inputBagOverride_multiqc_data.json
expire_in: 7 days
retry:
max: 0
@@ -815,13 +815,13 @@ override_fastq:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
- - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
- - pytest -m completionMultiqc --filename fastqOverride_PE_multiqc_data.json
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
+ - pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- - fastqOverride_PE_multiqc_data.json
+ - fastqOverride_multiqc_data.json
expire_in: 7 days
retry:
max: 0
@@ -838,13 +838,13 @@ override_species:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --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
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
+ - pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- - speciesOverride_PE_multiqc_data.json
+ - speciesOverride_multiqc_data.json
expire_in: 7 days
retry:
max: 0
@@ -861,13 +861,13 @@ override_stranded:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
- - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_PE_multiqc_data.json \;
- - pytest -m completionMultiqc --filename strandedOverride_PE_multiqc_data.json
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
+ - pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- - strandedOverride_PE_multiqc_data.json
+ - strandedOverride_multiqc_data.json
expire_in: 7 days
retry:
max: 0
@@ -884,13 +884,13 @@ override_spike:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --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
+ - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
+ - pytest -m completionMultiqc --filename spikeOverride_multiqc_data
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- - spikedOverride_PE_multiqc_data.json
+ - spikedOverride_multiqc_data.json
expire_in: 7 days
retry:
max: 0
--
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