From 8859d7e913b9def9ba39164cc6ef3201081d2363 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 28 Jan 2021 15:06:06 -0600
Subject: [PATCH] Add multiqc html to ci artifacts for override tests
---
.gitlab-ci.yml | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f794c79..70dff50 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -793,12 +793,14 @@ override_inputBag:
- 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_multiqc_data.json \;
+ - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./inputBagOverride_multiqc.html \;
- pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- inputBagOverride_multiqc_data.json
+ - inputBagOverride_multiqc.html
expire_in: 7 days
retry:
max: 0
@@ -816,12 +818,14 @@ override_fastq:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
+ - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./fastqOverride_multiqc.html \;
- pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- fastqOverride_multiqc_data.json
+ - fastqOverride_multiqc.html
expire_in: 7 days
retry:
max: 0
@@ -839,12 +843,14 @@ override_species:
- 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_multiqc_data.json \;
+ - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./speciesOverride_multiqc.html \;
- pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- speciesOverride_multiqc_data.json
+ - speciesOverride_multiqc.html
expire_in: 7 days
retry:
max: 0
@@ -862,12 +868,14 @@ override_stranded:
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
+ - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./strandedOverride_multiqc.html \;
- pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- strandedOverride_multiqc_data.json
+ - strandedOverride_multiqc.html
expire_in: 7 days
retry:
max: 0
@@ -885,12 +893,14 @@ override_spike:
- 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_multiqc_data.json \;
+ - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./spikeOverride_multiqc.html \;
- pytest -m completionMultiqc --filename spikeOverride_multiqc_data
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- spikedOverride_multiqc_data.json
+ - spikeOverride_multiqc.html
expire_in: 7 days
retry:
max: 0
--
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