Add multiqc html to ci artifacts for override tests

.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